diff --git a/.editorconfig b/.editorconfig
index 15d11df6..72dda289 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -31,8 +31,3 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
-
-# ignore parameters.md
-[parameters.md]
-trim_trailing_whitespace = false
-indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index e756a668..98343750 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -16,7 +16,7 @@ If you'd like to write some code for genomic-medicine-sweden/nallo, the standard
 1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/nallo issues](https://github.com/genomic-medicine-sweden/nallo/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/nallo repository](https://github.com/genomic-medicine-sweden/nallo) 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).
+4. Use `nf-core pipelines 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
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -36,14 +36,14 @@ There are typically two types of tests that run:
 
 ### Lint tests
 
-Altough this is not a `nf-core` pipeline, `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all their pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, they have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+Although this is not a `nf-core` pipeline, `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all their pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, they have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline tests
 
-This pipeline should be set up with a minimal set of test-data.
+This pipeline is set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
@@ -68,22 +68,23 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+10. Update the tool references `assets/software_references.yml`.
+11. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-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.
+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/main/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 `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -96,7 +97,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index a054825b..e1156a08 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,46 +9,34 @@ 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 genomic-medicine-sweden/nallo _(eg. 1.1, 1.5, 1.8.2)_
-
-        "
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index d50d1ea0..a0f36f7c 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medi
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/nallo/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines 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.
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
new file mode 100644
index 00000000..f2f1b4da
--- /dev/null
+++ b/.github/workflows/build-docs.yml
@@ -0,0 +1,43 @@
+name: build docs
+# https://github.com/nf-cmgg/structural/blob/master/.github/workflows/build-docs.yml
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - name: Obtain version from nextflow config
+        run: |
+          version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)
+          [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version
+          echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
+      - name: Setup git user
+        run: |
+          git config --global user.name "${{github.actor}}"
+          git config --global user.email "${{github.actor}}@users.noreply.github.com"
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - name: Install dependencies
+        run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
+      - name: Build docs
+        run: |
+          [[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} || mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+      - name: Set default docs
+        run: mike set-default --push latest
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fe701aed..7c466c2a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -7,9 +7,13 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NFTEST_VER: "0.9.2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -20,88 +24,55 @@ permissions:
 
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - ""
-          - "--preset ONT_R10 --input https://github.com/genomic-medicine-sweden/test-datasets/raw/e2266a34c14d1e0a9ef798de3cd81a76c9216fc1/testdata/samplesheet_multisample_bam_ont.csv --parallel_alignments 2 --parallel_snv 1"
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-  nftest:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: ${{ matrix.tags }} | ${{ matrix.profile }} | NF-${{ matrix.NXF_VER }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
+          - "24.04.2"
           - "latest-everything"
-          - "23.04.0"
         tags:
-          - "SHORT_VARIANT_CALLING"
-          - "SNV_ANNOTATION"
           - "samplesheet"
           - "samplesheet_multisample_bam"
+          - "samplesheet_multisample_ont_bam"
+          - "SHORT_VARIANT_CALLING"
+          - "SNV_ANNOTATION"
+          - "CALL_SVS"
+          - "ANNOTATE_SVS"
+          - "RANK_VARIANTS"
+          - "CALL_REPEAT_EXPANSIONS"
+          - "METHYLATION"
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        with:
+          fetch-depth: 0
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
       - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
+          install-pdiff: true
 
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
           architecture: "x64"
 
-      - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always() # always run even if the previous step fails
-        with:
-          report_paths: test.xml
+          nf-test test \
+            --ci \
+            --changed-since HEAD^ \
+            --verbose \
+            --tag ${{ matrix.tags }} \
+            --profile "+${{ matrix.profile }}" \
+            --junitxml=test.xml
diff --git a/.github/workflows/ci_master.yml b/.github/workflows/ci_master.yml
index 2de564cd..a2ee5d35 100644
--- a/.github/workflows/ci_master.yml
+++ b/.github/workflows/ci_master.yml
@@ -39,7 +39,7 @@ jobs:
         parameters:
           - "--bed=`null`"
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d644..713dc3e7 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines 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-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/keep_a_changelog.yml b/.github/workflows/keep_a_changelog.yml
new file mode 100644
index 00000000..952f2e54
--- /dev/null
+++ b/.github/workflows/keep_a_changelog.yml
@@ -0,0 +1,15 @@
+name: "Changelog Reminder"
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dangoslen/changelog-enforcer@v3
+        with:
+          changeLogPath: "CHANGELOG.md"
+          skipLabels: "Skip-Changelog"
diff --git a/.github/workflows/linting b/.github/workflows/linting
new file mode 100644
index 00000000..e69de29b
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe88..a502573c 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f..42e519bf 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@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 00000000..352649ae
--- /dev/null
+++ b/.github/workflows/template_version_comment.yml
@@ -0,0 +1,45 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Read template version from .nf-core.yml
+        uses: nichmor/minimal-read-yaml@v0.0.2
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          contains(env.OUTPUT, 'nf-core')
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
diff --git a/.gitignore b/.gitignore
index 2eef655b..23b0c7de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+null/
 .nf-test*
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a1821..46118637 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,14 @@ 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
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - 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 cb773092..21fc7d81 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,7 @@
+bump_version: null
 lint:
   files_exist:
+    - CITATIONS.md
     - CODE_OF_CONDUCT.md
     - assets/nf-core-nallo_logo_light.png
     - docs/README.md
@@ -9,6 +11,7 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/modules.config
+    - conf/igenomes_ignored.config
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-nallo_logo_light.png
@@ -18,14 +21,23 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - .github/CONTRIBUTING.md
     - .prettierignore
+  modules_config: false
   multiqc_config:
     - report_comment
   nextflow_config:
     - manifest.name
     - manifest.homePage
-  modules_config: false
-nf_core_version: 2.14.1
+nf_core_version: 3.0.2
+org_path: null
 repository_type: pipeline
 template:
-  prefix: genomic-medicine-sweden
-  skip: []
+  author: Felix Lenner
+  description: Long-read variant calling pipeline
+  force: false
+  is_nfcore: false
+  name: nallo
+  org: genomic-medicine-sweden
+  outdir: .
+  skip_features: []
+  version: 0.4.0dev
+update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1dc..9e9f0e1c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 547dbbe9..e4b0fd26 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,19 +3,214 @@
 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).
 
-## v0.3.2 - [2024-09-20]
+## 0.4.0 - [2025-01-15]
+
+### `Added`
+
+- [#345](https://github.com/genomic-medicine-sweden/nallo/pull/345) - Added first version of a metro map
+- [#346](https://github.com/genomic-medicine-sweden/nallo/pull/346) - Added nf-test to call_svs
+- [#351](https://github.com/genomic-medicine-sweden/nallo/pull/351) - Added sample name to sniffles2 VCF
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Added (hidden) `params.extra_<tool>_options` for the test profile to modkit, vep, paraphase and hifiasm
+- [#356](https://github.com/genomic-medicine-sweden/nallo/pull/356) - Added missing SNV and PED file to output documentation
+- [#363](https://github.com/genomic-medicine-sweden/nallo/pull/363) - Added Zenodo link
+- [#366](https://github.com/genomic-medicine-sweden/nallo/pull/366) - Added sorting of samples when creating PED files, so the output is always the same
+- [#367](https://github.com/genomic-medicine-sweden/nallo/pull/367) - Added Severus as the default SV caller, together with a `--sv_caller` parameter to choose caller
+- [#371](https://github.com/genomic-medicine-sweden/nallo/pull/371) - Added `FOUND_IN=caller` tags to SV output
+- [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Added longphase as the default phaser
+- [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Added single-sample tbi output to the short variant calling subworkflow
+- [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Added a new `--minimap2_read_mapping_preset` parameter
+- [#403](https://github.com/genomic-medicine-sweden/nallo/pull/403) - Added `FOUND_IN=hificnv` tags to CNV calling output
+- [#408](https://github.com/genomic-medicine-sweden/nallo/pull/408) - Added a new subworkflow to annotate SVs
+- [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Added `FOUND_IN=deepvariant` tags to SNV calling output
+- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Added a check for unique input filenames for each sample
+- [#419](https://github.com/genomic-medicine-sweden/nallo/pull/419) - Added support for SV filtering using input BED file ([#348](https://github.com/genomic-medicine-sweden/nallo/issues/348))
+- [#429](https://github.com/genomic-medicine-sweden/nallo/pull/429) - Added nf-test to CNV calling
+- [#429](https://github.com/genomic-medicine-sweden/nallo/pull/429) - Added SVDB to merge CNV calling results
+- [#430](https://github.com/genomic-medicine-sweden/nallo/pull/430) - Added a GitHub action to build and publish docs to GitHub Pages
+- [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Added files needed to automatically build and publish docs to GitHub Pages
+- [#435](https://github.com/genomic-medicine-sweden/nallo/pull/435) - Added nf-test to rank variants
+- [#445](https://github.com/genomic-medicine-sweden/nallo/pull/445) - Added FOUND_IN tag and nf-test to rank variants
+- [#446](https://github.com/genomic-medicine-sweden/nallo/pull/446) - Added the vcfstatsreport from DeepVariant to snv calling
+- [#450](https://github.com/genomic-medicine-sweden/nallo/pull/450) - Added ranking of SVs (and CNVs)
+- [#451](https://github.com/genomic-medicine-sweden/nallo/pull/451) - Added support for running methylation subworkflow without phasing
+- [#451](https://github.com/genomic-medicine-sweden/nallo/pull/451) - Added nf-test to methylation
+- [#491](https://github.com/genomic-medicine-sweden/nallo/pull/491) - Added a changelog reminder action
+- [#496](https://github.com/genomic-medicine-sweden/nallo/pull/496) - Added a subworkflow to filter variants
+
+### `Changed`
+
+- [#344](https://github.com/genomic-medicine-sweden/nallo/pull/344) - Changed version to 0.4.0dev
+- [#346](https://github.com/genomic-medicine-sweden/nallo/pull/346) - Renamed structural_variant_calling to call_svs
+- [#351](https://github.com/genomic-medicine-sweden/nallo/pull/351) - Changed from using sniffles to bcftools to merge SV calls from multiple samples
+- [#351](https://github.com/genomic-medicine-sweden/nallo/pull/351) - Renamed the structural variant output files and directories
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Changed fastq conversion to run only when the assembly workflow is active
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Changed FastQC to run on BAM files to remove concatenation of fastq files
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Changed FastQC from the main workflow to QC_ALIGNED_READS, updated output directories and documentation
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Combined `--skip_raw_read_qc` and `--skip_aligned_read_qc` parameters into `--skip_qc`
+- [#355](https://github.com/genomic-medicine-sweden/nallo/pull/355) - Updated paraphase to compress and index VCFs within the module
+- [#365](https://github.com/genomic-medicine-sweden/nallo/pull/365) - Changed CI to only use nf-test for pipeline tests
+- [#381](https://github.com/genomic-medicine-sweden/nallo/pull/381) - Updated CI nf-test version to 0.9.0
+- [#382](https://github.com/genomic-medicine-sweden/nallo/pull/382) - Changed vep_plugin_files description in schema and docs
+- [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Changed phasing output structure and naming, and updated docs
+- [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Changed the default minimap2 preset for PacBio data from `map-hifi` to `lr:hqae`
+- [#397](https://github.com/genomic-medicine-sweden/nallo/pull/397) - Changed `pipelines_testdata_base_path` to pin a specific commit
+- [#402](https://github.com/genomic-medicine-sweden/nallo/pull/402) - Updated broken test profile link added in [#397](https://github.com/genomic-medicine-sweden/nallo/pull/397)
+- [#403](https://github.com/genomic-medicine-sweden/nallo/pull/403) - Changed `ADD_FOUND_IN_TAG` process to allow input files to be named the same as output, fixed header line description and removed bcftools view versions in header
+- [#403](https://github.com/genomic-medicine-sweden/nallo/pull/403) - Revert [#404](https://github.com/genomic-medicine-sweden/nallo/pull/404)
+- [#404](https://github.com/genomic-medicine-sweden/nallo/pull/404) - Changed to only run nf-tests where files have changes compared to the base branch
+- [#407](https://github.com/genomic-medicine-sweden/nallo/pull/407) - Changed echtvar example file in docs
+- [#410](https://github.com/genomic-medicine-sweden/nallo/pull/410) - Updated genmod to version 3.8.3
+- [#411](https://github.com/genomic-medicine-sweden/nallo/pull/411) - Updated longphase module to most recent version. ([#409](https://github.com/genomic-medicine-sweden/nallo/issues/409)).
+- [#416](https://github.com/genomic-medicine-sweden/nallo/pull/416) - Updated WhatsHap to 2.3 and added the `--use-supplementary` flag to use supplementary reads for phasing by default. Changed modules to use biocontainers instead of custom containers. ([#296](https://github.com/genomic-medicine-sweden/nallo/issues/296))
+- [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Updated SNV annotation tests to use correct configuration, and snapshot the md5sum, and summary of the variants
+- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the default value of `--alignment_processes` from 1 to 8, meaning the pipeline will perform parallel alignment by default
+- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the order of input files to samtools merge to be sorted on filename, avoiding unstable nf-test snapshots
+- [#422](https://github.com/genomic-medicine-sweden/nallo/pull/422) - Updated nf-core/tools template to v3.0.1
+- [#423](https://github.com/genomic-medicine-sweden/nallo/pull/423) - Updated metro map
+- [#428](https://github.com/genomic-medicine-sweden/nallo/pull/428) - Changed from using bcftools to SVDB for SV merging
+- [#429](https://github.com/genomic-medicine-sweden/nallo/pull/429) - Updated HiFiCNV to 1.0.0
+- [#429](https://github.com/genomic-medicine-sweden/nallo/pull/429) - Refactored the CNV calling subworkflow
+- [#429](https://github.com/genomic-medicine-sweden/nallo/pull/429) - Changed SV and CNV calling outputs, merging is now done per family
+- [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Changed `CITATIONS.md` to `docs/CITATIONS.md`,
+- [#433](https://github.com/genomic-medicine-sweden/nallo/pull/433) - Updated docs and README.
+- [#434](https://github.com/genomic-medicine-sweden/nallo/pull/434) - Updated the SVDB merge module to fix unstable CALL_SVS tests
+- [#435](https://github.com/genomic-medicine-sweden/nallo/pull/435) - Updated and refactored processes and workflows related to variant ranking
+- [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Updated pipeline tests to use functions in nft-utils instead of checking hardcoded paths
+- [#440](https://github.com/genomic-medicine-sweden/nallo/pull/440) - Updated hifiasm to 0.20 with new default parameters for telomeres and scaffolding ([#295](https://github.com/genomic-medicine-sweden/nallo/issues/295))
+- [#441](https://github.com/genomic-medicine-sweden/nallo/pull/441) - Changed the minimap2 preset for hifi reads back to `map-hifi`
+- [#443](https://github.com/genomic-medicine-sweden/nallo/pull/443) - Refactored reference channel assignments
+- [#443](https://github.com/genomic-medicine-sweden/nallo/pull/443) - Updated schemas for `vep_plugin_files` and `snp_db`
+- [#451](https://github.com/genomic-medicine-sweden/nallo/pull/451) - Simplified methylation subworkflow
+- [#474](https://github.com/genomic-medicine-sweden/nallo/pull/474) - Updated VEP and CADD channels to fix bugs introduced in [#443](https://github.com/genomic-medicine-sweden/nallo/pull/443)
+- [#479](https://github.com/genomic-medicine-sweden/nallo/pull/479) - Replaced bgzip tabix with bcftools sort in rank variants to fix [#457](https://github.com/genomic-medicine-sweden/nallo/issues/457)
+- [#480](https://github.com/genomic-medicine-sweden/nallo/pull/480) - Updated ranking of SVs to work with multiple families per project
+- [#484](https://github.com/genomic-medicine-sweden/nallo/pull/484) - Updated metro map and added SVG version
+- [#485](https://github.com/genomic-medicine-sweden/nallo/pull/485) - Updated repeat expansion annotation to annotate per family instead of per sample
+- [#486](https://github.com/genomic-medicine-sweden/nallo/pull/486) - Updated nf-core modules
+- [#487](https://github.com/genomic-medicine-sweden/nallo/pull/487) - Changed CI tests to only run tests where changes have been made
+- [#488](https://github.com/genomic-medicine-sweden/nallo/pull/488) - Changed naming of input parameters
+- [#489](https://github.com/genomic-medicine-sweden/nallo/pull/489) - Updated nf-core template to 3.0.2
+- [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Refactored `nallo.nf` to remove many nested ifs and easier to follow logic
+- [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Updated rank_variants dependencies with sv_annotation
+- [#498](https://github.com/genomic-medicine-sweden/nallo/pull/498) - Updated CI to fix CI failures after merge
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed to annotating and ranking SNVs per family instead of per project
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed output documentation and structure to match `sample` and `family` for all variants
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed the way of validating the samplesheet to remove outputing false errors with `ifEmpty`
+- [#505](https://github.com/genomic-medicine-sweden/nallo/pull/505) - Updated TRGT to 1.2.0
+- [#506](https://github.com/genomic-medicine-sweden/nallo/pull/506) - Updated documentation
+- [#507](https://github.com/genomic-medicine-sweden/nallo/pull/507) - Changed the default value of `ch_hgnc_ids` to allow running without `--filter_variants_hgnc_ids` introduced in [#496](https://github.com/genomic-medicine-sweden/nallo/pull/443)
+- [#509](https://github.com/genomic-medicine-sweden/nallo/pull/509) - Updated documentation to fix mistakes
+- [#510](https://github.com/genomic-medicine-sweden/nallo/pull/510) - Changed the MultiQC methods description to update dynamically based on `ch_versions`
+- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed one `single_sample` to `sample` and one `multi_sample` to `family` output directories missed in [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502)
+- [#512](https://github.com/genomic-medicine-sweden/nallo/pull/512) - Changed all `*_snv_*` to `*_snvs_*` for published output files to match `snvs`, `cnvs`, `svs` and `repeats`.
+- [#513](https://github.com/genomic-medicine-sweden/nallo/pull/513) - Updated CITATIONS.md link in README
+- [#523](https://github.com/genomic-medicine-sweden/nallo/pull/523) - Updated to filter more than one family per run, missed in [#496](https://github.com/genomic-medicine-sweden/nallo/pull/496)
+
+### `Removed`
+
+- [#352](https://github.com/genomic-medicine-sweden/nallo/pull/352) - Removed the fqcrs module
+- [#356](https://github.com/genomic-medicine-sweden/nallo/pull/356) - Removed filter_vep section from output documentation since it is not in the pipeline
+- [#379](https://github.com/genomic-medicine-sweden/nallo/pull/379) - Removed VEP Plugins from testdata ([genomic-medicine-sweden/test-datasets#16](https://github.com/genomic-medicine-sweden/test-datasets/pull/16))
+- [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Removed support for co-phasing SVs with HiPhase, as the officially supported caller (pbsv) is not in the pipeline
+- [#412](https://github.com/genomic-medicine-sweden/nallo/pull/412) - Removed `bcftools/index`, as indexing is handled by other modules and no references remained. ([#377](https://github.com/genomic-medicine-sweden/nallo/issues/377))
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Removed support for automatically creating an echvar database with SNVs and INDELs
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Removed `containts_affected` logic from the snv-calling workflow, since this was previously changed to be checked before pipeline start
+
+### `Fixed`
+
+- [#370](https://github.com/genomic-medicine-sweden/nallo/pull/370) - Fixed unsorted variants in SNV outputs ([#362](https://github.com/genomic-medicine-sweden/nallo/issues/362))
+- [#381](https://github.com/genomic-medicine-sweden/nallo/pull/381) - Fixed `--vep_cache` not working as expected with tar.gz cache downloaded from VEP, updated testdata in [genomic-medicine-sweden/test-datasets#17](https://github.com/genomic-medicine-sweden/test-datasets/pull/17)
+- [#382](https://github.com/genomic-medicine-sweden/nallo/pull/382) - Fixed broken links and formatting in documentation
+- [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Fixed minimap2 preset for ONT data being overwritten to `map-ont` when it should have been `lr:hq`, due to different settings in index and alignment processes [#392](https://github.com/genomic-medicine-sweden/nallo/issues/392)
+- [#402](https://github.com/genomic-medicine-sweden/nallo/pull/402) - Fixed double sample names in HiFiCNV output
+- [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Fixed missing/malformed software versions in `ADD_FOUND_IN_TAG`, `ADD_MOST_SEVERE_CSQ`, `ADD_MOST_SEVERE_PLI`, `SAMPLESHEET_PED`, `SOMALIER_PED` and `TRGT`
+- [#444](https://github.com/genomic-medicine-sweden/nallo/pull/444) - Fixed genmod assigning wrong models on chromosome X when named `chrX` ([#343](https://github.com/genomic-medicine-sweden/nallo/issues/343))
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Fixed genmod only scoring compounds in one family [#501](https://github.com/genomic-medicine-sweden/nallo/issues/501)
+
+### Parameters
+
+| Old parameter                    | New parameter                     |
+| -------------------------------- | --------------------------------- |
+| `--skip_aligned_read_qc`         | `--skip_qc`                       |
+| `--skip_raw_read_qc`             | `--skip_qc`                       |
+|                                  | `--sv_caller`                     |
+|                                  |  `--minimap2_read_mapping_preset` |
+| `--genome`                       |                                   |
+| `--igenomes_ignore`              |                                   |
+| `--max_cpus`                     |                                   |
+| `--max_memory`                   |                                   |
+| `--max_time`                     |                                   |
+| `--validationShowHiddenParams`   |                                   |
+| `--validationSkipDuplicateCheck` |                                   |
+| `--validationS3PathCheck`        |                                   |
+| `--monochromeLogs`               | `--monochrome_logs`               |
+|                                  | `--filter_variants_hgnc_ids`      |
+|                                  | `--filter_snvs_expression`        |
+|                                  | `--filter_svs_expression`         |
+| `--skip_short_variant_calling`   | `--skip_snv_calling`              |
+| `--skip_assembly_wf`             | `--skip_genome_assembly`          |
+| `--skip_mapping_wf`              | `--skip_alignment`                |
+| `--skip_methylation_wf`          | `--skip_methylation_pileups`      |
+| `--skip_phasing_wf`              | `--skip_phasing`                  |
+| `--variant_caller`               | `--snv_caller`                    |
+| `--parallel_snv`                 | `--snv_calling_processes`         |
+| `--cadd_prescored`               | `--cadd_prescored_indels`         |
+| `--snp_db`                       | `--echtvar_snv_databases`         |
+| `--variant_catalog`              | `--stranger_repeat_catalog`       |
+| `--bed`                          | `--target_regions`                |
+| `--hificnv_xy`                   | `--hificnv_expected_xy_cn`        |
+| `--hificnv_xx`                   | `--hificnv_expected_xx_cn`        |
+| `--hificnv_exclude`              | `--hificnv_excluded_regions`      |
+| `--reduced_penetrance`           | `--genmod_reduced_penetrance`     |
+| `--score_config_snv`             | `--genmod_score_config_snvs`      |
+| `--score_config_sv`              | `--genmod_score_config_svs`       |
+| `--parallel_alignments`          | `--alignment_processes`           |
+| `--svdb_dbs`                     | `--svdb_sv_databases`             |
+
+> [!NOTE]
+> Parameter has been updated if both old and new parameter information is present.
+> Parameter has been added if just the new parameter information is present.
+> Parameter has been removed if new parameter information isn't present.
+
+### Module updates
+
+| Tool                  | Old version | New version |
+| --------------------- | ----------- | ----------- |
+| fqcrs                 | 0.1.0       |
+| severus               |             | 1.1         |
+| longphase             |             | 1.7.3       |
+| genmod                | 3.8.2       | 3.9         |
+| WhatsHap              | 2.2         | 2.3         |
+| SVDB                  |             | 2.8.2       |
+| hifiasm               | 0.19.8      | 0.20.0      |
+| HiFiCNV               | 0.1.7       | 1.0.0       |
+| samtools/faidx        | 1.2         | 1.21        |
+| samtools/index        | 1.2         | 1.21        |
+| samtools/merge        | 1.2         | 1.21        |
+| stranger              | 0.9.1       | 0.9.2       |
+| multiqc               | 1.21        | 1.25.1      |
+| ensemblvep/filter_vep |             | 113         |
+| TRGT                  | 0.4.0       | 1.2.0       |
+| bcftools/merge        | 1.2         |             |
+
+> [!NOTE]
+> Version has been updated if both old and new version information is present.
+> Version has been added if just the new version information is present.
+> Version has been removed if new version information isn't present.
+
+## 0.3.2 - [2024-09-20]
 
 ### `Fixed`
 
 - [#396](https://github.com/genomic-medicine-sweden/nallo/pull/396) - Fixed the release test profile not working, by pinning the testdata used [#395](https://github.com/genomic-medicine-sweden/nallo/issues/395)
 
-## v0.3.1 - [2024-09-11]
+## 0.3.1 - [2024-09-11]
 
 ### `Fixed`
 
 - [#359](https://github.com/genomic-medicine-sweden/nallo/pull/359) - Fixed single sample SNV VCFs containing variants from all samples, resuling in a large number of empty GT calls
 
-## v0.3.0 - [2024-08-29]
+## 0.3.0 - [2024-08-29]
 
 ### `Added`
 
@@ -99,6 +294,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#252](https://github.com/genomic-medicine-sweden/nallo/pull/252) - Fixed duplicate SNVs in outputs when providing a BED-regions with overlapping regions
 - [#267](https://github.com/genomic-medicine-sweden/nallo/pull/267) - Fixed warning where `MODKIT_PILEUP_HAPLOTYPES` would be defined more than once
 - [#300](https://github.com/genomic-medicine-sweden/nallo/pull/300) - Fixed missing paraphase version
+- [#427](https://github.com/genomic-medicine-sweden/nallo/pull/427) - Fixed duplicate RG tags in BAM files after mapping from uBAMs ([#426](https://github.com/genomic-medicine-sweden/nallo/issues/426)).
 
 ### Parameters
 
@@ -141,7 +337,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | splitubam                   |             | 0.1.1       |
 | fastp                       | 0.23.4      |             |
 
-## v0.2.0 - [2024-06-26]
+> [!NOTE]
+> Version has been updated if both old and new version information is present.
+> Version has been added if just the new version information is present.
+> Version has been removed if new version information isn't present.
+
+## 0.2.0 - [2024-06-26]
 
 ### `Added`
 
@@ -228,7 +429,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 > Version has been added if just the new version information is present.
 > Version has been removed if new version information isn't present.
 
-## v0.1.0 - [2024-05-08]
+## 0.1.0 - [2024-05-08]
 
 Initial release of genomic-medicine-sweden/nallo, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index f22658d0..f7188289 100644
--- a/README.md
+++ b/README.md
@@ -1,52 +1,58 @@
 [![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)
 [![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/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13748210.svg)](https://doi.org/10.5281/zenodo.13748210)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![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 Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/genomic-medicine-sweden/nallo)
 
 ## Introduction
 
-**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-read rare disease SV/SNV identification using both PacBio and (targeted) ONT-data. Heavily influenced by best-practice pipelines such as [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf).
+**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf).
+
+<picture align="center">
+    <img alt="genomic-medicine-sweden/nallo workflow" src="docs/images/nallo_metromap.png">
+  </picture>
 
 ## Pipeline summary
 
 ##### QC
 
-- FastQC ([`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-- Aligned read QC ([`cramino`](https://github.com/wdecoster/cramino))
-- Depth information ([`mosdepth`](https://github.com/brentp/mosdepth))
+- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino) and [mosdepth](https://github.com/brentp/mosdepth)
 
 ##### Alignment & assembly
 
-- Align reads to reference ([`minimap2`](https://github.com/lh3/minimap2))
-- Assemble (trio-binned) haploid genomes (HiFi only) ([`hifiasm`](https://github.com/chhylp123/hifiasm))
+- Align reads to reference with [minimap2](https://github.com/lh3/minimap2)
+- Assemble haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm) (HiFi only)
 
 ##### Variant calling
 
-- Short variant calling & joint genotyping of SNVs ([`deepvariant`](https://github.com/google/deepvariant) + [`GLNexus`](https://github.com/dnanexus-rnd/GLnexus))
-- SV calling and joint genotyping ([`sniffles2`](https://github.com/fritzsedlazeck/Sniffles))
-- Tandem repeats (HiFi only) ([`TRGT`](https://github.com/PacificBiosciences/trgt/tree/main))
-- Assembly based variant calls (HiFi only) ([`dipcall`](https://github.com/lh3/dipcall))
-- CNV-calling ([`HiFiCNV`](https://github.com/PacificBiosciences/HiFiCNV))
-- Call paralogous genes ([`Paraphase`](https://github.com/PacificBiosciences/paraphase))
+- Call SNVs & joint genotyping with [deepvariant](https://github.com/google/deepvariant) and [GLNexus](https://github.com/dnanexus-rnd/GLnexus)
+- Call SVs with [Severus](https://github.com/KolmogorovLab/Severus) or [Sniffles2](https://github.com/fritzsedlazeck/Sniffles)
+- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)
+- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only)
+- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase)
+- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall) (HiFi only)
 
 ##### Phasing and methylation
 
-- Phase and haplotag reads ([`whatshap`](https://github.com/whatshap/whatshap) + [`hiphase`](https://github.com/PacificBiosciences/HiPhase))
-- Methylation pileups ([`modkit`](https://github.com/nanoporetech/modkit))
+- Phase and haplotag reads with [LongPhase](https://github.com/twolinin/longphase), [whatshap](https://github.com/whatshap/whatshap) or [HiPhase](https://github.com/PacificBiosciences/HiPhase)
+- Create methylation pileups with [modkit](https://github.com/nanoporetech/modkit)
 
 ##### Annotation
 
-- Annotate SNVs and INDELs with database(s) of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. ([`echtvar`](https://github.com/brentp/echtvar) and [`VEP`](https://github.com/Ensembl/ensembl-vep))
+- Annotate SNVs and INDELs with databases of choice, e.g. [gnomAD](https://gnomad.broadinstitute.org), [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/), [CADD](https://cadd.gs.washington.edu) with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep)
 - Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger)
+- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep)
+
+##### Ranking
 
-##### Filtering and ranking
+- Rank SNVs, INDELs, SVs and CNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)
 
-- Rank variants ([`GENMOD`](https://github.com/Clinical-Genomics/genmod))
+##### Filtering
+
+- Filter SNVs, INDELs, SVs and CNVs with [filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html)
 
 ## Usage
 
@@ -59,31 +65,22 @@ Prepare a samplesheet with input data:
 
 ```
 project,sample,file,family_id,paternal_id,maternal_id,sex,phenotype
-testrun,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2
-testrun,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1
+NIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2
+NIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1
 ```
 
-Now, you can run the pipeline using:
+Supply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using:
 
 ```bash
-nextflow run genomic-medicine-sweden/nallo -profile YOURPROFILE \
+nextflow run genomic-medicine-sweden/nallo \
+    -profile <docker/singularity/.../institute> \
     --input samplesheet.csv \
     --preset <revio/pacbio/ONT_R10> \
     --fasta <reference.fasta> \
     --outdir <OUTDIR>
 ```
 
-For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/nallo/blob/dev/docs/usage.md).
-
-> [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-
-To run in an offline environment, download the pipeline and singularity images using [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use):
-
-```
-nf-core download genomic-medicine-sweden/nallo
-```
+For more details and further functionality, please refer to the [documentation](http://genomic-medicine-sweden.github.io/nallo/).
 
 ## Credits
 
@@ -97,7 +94,9 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 ## Citations
 
-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).
+If you use genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.13748210](https://doi.org/10.5281/zenodo.13748210).
+
+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/main/LICENSE).
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >
@@ -105,4 +104,4 @@ This pipeline uses code and infrastructure developed and maintained by the [nf-c
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
 
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+An extensive list of references for the tools used by the pipeline can be found in the [`docs/CITATIONS.md`](docs/CITATIONS.md) file.
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 9d78bfcd..d8195c2e 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,21 +3,11 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "genomic-medicine-sweden/nallo Methods Description"
 section_href: "https://github.com/genomic-medicine-sweden/nallo"
 plot_type: "html"
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using genomic-medicine-sweden/nallo v${workflow.manifest.version} ${doi_text} which uses the nf-core template (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using genomic-medicine-sweden/nallo v${workflow.manifest.version} ${doi_text} which uses uses code and infrastructure developed and maintained by the nf-core community, reused here under the <a href="https://github.com/nf-core/tools/blob/master/LICENSE">MIT licence</a> (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
-  <p>${tool_citations}</p>
-  <h4>References</h4>
-  <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
-    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
-    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
-    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
-    ${tool_bibliography}
-  </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>
     <ul>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 24af127c..125517b7 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,8 +1,6 @@
 report_comment: >
-
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.3.1" target="_blank">genomic-medicine-sweden/nallo</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.4.0" target="_blank">genomic-medicine-sweden/nallo</a>
   analysis pipeline.
-
 report_section_order:
   "genomic-medicine-sweden-nallo-methods-description":
     order: -1000
diff --git a/assets/schema_hgnc_ids.json b/assets/schema_hgnc_ids.json
new file mode 100644
index 00000000..2f3e64e1
--- /dev/null
+++ b/assets/schema_hgnc_ids.json
@@ -0,0 +1,26 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_hgnc_ids.json",
+    "title": "genomic-medicine-sweden/nallo pipeline - params.filter_variants_hgnc_ids schema",
+    "description": "Schema for the file provided with params.filter_variants_hgnc_ids",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "hgnc_id": {
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+$"
+                    },
+                    {
+                        "type": "integer"
+                    }
+                ],
+                "exists": true,
+                "errorMessage": "HGNC IDs must exist with a header line `hgnc_id`, then one HGNC ID per line, either as e.g. `4826` or `HGNC:4826`."
+            }
+        },
+        "required": ["hgnc_id"]
+    }
+}
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 46c00ba6..81e7e095 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_input.json",
     "title": "genomic-medicine-sweden/nallo pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -26,14 +26,30 @@
                 "meta": ["family_id"]
             },
             "paternal_id": {
-                "type": "string",
-                "pattern": "^\\S+$",
+                "oneOf": [
+                    {
+                        "type": "integer",
+                        "enum": [0]
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^(\\S+)$"
+                    }
+                ],
                 "errorMessage": "Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use 0.",
                 "meta": ["paternal_id"]
             },
             "maternal_id": {
-                "type": "string",
-                "pattern": "^\\S+$",
+                "oneOf": [
+                    {
+                        "type": "integer",
+                        "enum": [0]
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^(\\S+)$"
+                    }
+                ],
                 "errorMessage": "Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use 0.",
                 "meta": ["maternal_id"]
             },
diff --git a/assets/schema_snp_db.json b/assets/schema_snp_db.json
new file mode 100644
index 00000000..61480f73
--- /dev/null
+++ b/assets/schema_snp_db.json
@@ -0,0 +1,24 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_snp_db.json",
+    "title": "genomic-medicine-sweden/nallo pipeline - params.echtvar_snv_databases schema",
+    "description": "Schema for the file provided with params.echtvar_snv_databases",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample must be provided and cannot contain spaces."
+            },
+            "file": {
+                "format": "file-path",
+                "type": "string",
+                "pattern": "^\\S+\\.zip$",
+                "errorMessage": "Echtvar database must be provided, cannot contain spaces and must have extension '.zip'"
+            }
+        },
+        "required": ["sample", "file"]
+    }
+}
diff --git a/assets/schema_snpdb.json b/assets/schema_snpdb.json
deleted file mode 100644
index 651ad58a..00000000
--- a/assets/schema_snpdb.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_gvcfs.json",
-    "title": "genomic-medicine-sweden/nallo pipeline - params.extra_gvcfs schema",
-    "description": "Schema for the file provided with params.extra_gvcfs",
-    "type": "array",
-    "items": {
-        "type": "object",
-        "properties": {
-            "sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
-            },
-            "file": {
-                "format": "file-path",
-                "type": "string",
-                "pattern": "^\\S+\\.zip$",
-                "errorMessage": "gVCF file must be provided, cannot contain spaces and must have extension 'g.vcf.gz' or 'gvcf.gz'"
-            }
-        },
-        "required": ["sample", "file"]
-    }
-}
diff --git a/assets/schema_vep_plugin_files.json b/assets/schema_vep_plugin_files.json
new file mode 100644
index 00000000..0be393a3
--- /dev/null
+++ b/assets/schema_vep_plugin_files.json
@@ -0,0 +1,20 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_vep_plugin_files.json",
+    "title": "genomic-medicine-sweden/nallo pipeline - params.vep_plugin_files schema",
+    "description": "Schema for the file provided with params.vep_plugin_files",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "vep_files": {
+                "format": "file-path",
+                "type": "string",
+                "pattern": "^\\S+",
+                "exists": true,
+                "errorMessage": "Vep plugin file must be a path and exist."
+            }
+        },
+        "required": ["vep_files"]
+    }
+}
diff --git a/assets/software_references.yml b/assets/software_references.yml
new file mode 100644
index 00000000..f5048133
--- /dev/null
+++ b/assets/software_references.yml
@@ -0,0 +1,139 @@
+tool:
+  nextflow:
+    citation: ""
+    bibliography: 'Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a>'
+  nf_core:
+    citation: ""
+    bibliography: 'Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a>'
+  bioconda:
+    citation: ""
+    bibliography: 'Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a>'
+  biocontainers:
+    citation: ""
+    bibliography: 'da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a>'
+  multiqc:
+    citation: "MultiQC (Ewels et al. 2016)"
+    bibliography: "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. PMID: 27312411; PMCID: PMC5039924."
+  add_most_severe_consequence:
+    citation: "add_most_severe_consequence (Neethiraj 2022)"
+    bibliography: ""
+  add_most_severe_pli:
+    citation: "add_most_severe_pli (Neethiraj 2022)"
+    bibliography: ""
+  bcftools:
+    citation: "BCFtools (Danecek et al. 2021)"
+    bibliography: "Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008"
+  bedtools:
+    citation: "BEDTools (Quinlan & Hall 2010)"
+    bibliography: "Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842."
+  bgzip:
+    citation: "bgzip"
+    bibliography: ""
+  busybox_awk:
+    citation: "BusyBox's awk"
+    bibliography: ""
+  cadd:
+    citation: "CADD (Rentzsch et al. 2019, Rentzsch et al. 2021)"
+    bibliography: "Rentzsch P, Schubach M, Shendure J, Kircher M. CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 2021;13(1):31. doi:10.1186/s13073-021-00835-9"
+  cramino:
+    citation: "cramino (De Coster & Rademakers 2023)"
+    bibliography: "Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311"
+  create_pedigree_file:
+    citation: "create_pedigree_file"
+    bibliography: ""
+  deepvariant:
+    citation: "DeepVariant (Poplin et al. 2018)"
+    bibliography: "Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235"
+  dipcall:
+    citation: "dipcall (Li et al. 2018)"
+    bibliography: "Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D (2018) A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods, 15:595-597. [PMID:30013044]"
+  echtvar:
+    citation: "Echtvar (Pedersen & de Ridder 2023)"
+    bibliography: "Brent S Pedersen, Jeroen de Ridder, Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels, Nucleic Acids Research, Volume 51, Issue 1, 11 January 2023, Page e3, https://doi.org/10.1093/nar/gkac931"
+  ensemblvep:
+    citation: "VEP (McLaren et al. 2016)"
+    bibliography: "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"
+  fastqc:
+    citation: "FastQC (Andrews 2010)"
+    bibliography: "Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+  gawk:
+    citation: "gawk"
+    bibliography: ""
+  genmod:
+    citation: "Genmod (Magnusson et al. 2018)"
+    bibliography: "Magnusson M, Hughes T, Glabilloy, Bitdeli Chef. genmod: Version 3.7.3. Published online November 15, 2018. doi:10.5281/ZENODO.3841142"
+  gfastats:
+    citation: "Gfastats (Formenti et al. 2022)"
+    bibliography: "Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, https://doi.org/10.1093/bioinformatics/btac460"
+  glnexus:
+    citation: "GLnexus (Yun et al. 2021)"
+    bibliography: "Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081"
+  gunzip:
+    citation: "gunzip"
+    bibliography: ""
+  hifiasm:
+    citation: "Hifiasm (Cheng et al. 2021)"
+    bibliography: "Cheng, H., Concepcion, G.T., Feng, X. et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5"
+  hificnv:
+    citation: "HiFiCNV"
+    bibliography: ""
+  hiphase:
+    citation: "HiPhase (Holt et al. 2024)"
+    bibliography: "James M Holt, Christopher T Saunders, William J Rowell, Zev Kronenberg, Aaron M Wenger, Michael Eberle, HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing, Bioinformatics, Volume 40, Issue 2, February 2024, btae042, https://doi.org/10.1093/bioinformatics/btae042"
+  longphase:
+    citation: "LongPhase (Lin et al. 2024)"
+    bibliography: "Jyun-Hong Lin, Liang-Chi Chen, Shu-Chi Yu, Yao-Ting Huang, LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants, Bioinformatics, Volume 38, Issue 7, March 2022, Pages 1816–1822, https://doi.org/10.1093/bioinformatics/btac058"
+  minimap2:
+    citation: "Minimap2 (Li 2018)"
+    bibliography: "Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191"
+  modkit:
+    citation: "modkit"
+    bibliography: ""
+  mosdepth:
+    citation: "mosdepth (Pedersen & Quinlan 2018)"
+    bibliography: "Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699"
+  paraphase:
+    citation: "Paraphase (Chen et al. 2023)"
+    bibliography: "Genome-wide profiling of highly similar paralogous genes using HiFi sequencing. Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M Devaney, Jessica Noya, April S Berlyoung, Rhonda Brandon, Kathleen S Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, UCI Genomics Research to Elucidate the Genetics of Rare Diseases (UCI GREGoR) Consortium, Michael A Eberle. bioRxiv 2024.04.19.590294; doi: https://doi.org/10.1101/2024.04.19.590294"
+  python:
+    citation: "Python (Van Rossum & Drake Jr 2009)"
+    bibliography: ""
+  samtools:
+    citation: "SAMtools (Danecek et al. 2021)"
+    bibliography: "Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008"
+  sniffles:
+    citation: "Sniffles2 (Smolka et al. 2024)"
+    bibliography: "Smolka, M., Paulin, L.F., Grochowski, C.M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02024-y"
+  severus:
+    citation: "Severus (Keskus et al. 2024)"
+    bibliography: "Ayse Keskus, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky, Ataberk Donmez, Lisa A. Lansdon, Isabel Rodriguez, Jimin Park, Yuelin Liu, Xiwen Cui, Joshua Gardner, Brandy McNulty, Samuel Sacco, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Daniel E. Cook, Pi-Chuan Chang, Alexey Kolesnikov, Andrew Carroll, Erin K. Molloy, Irina Pushel, Erin Guest, Tomi Pastinen, Kishwar Shafin, Karen H. Miga, Salem Malikic, Chi-Ping Day, Nicolas Robine, Cenk Sahinalp, Michael Dean, Midhat S. Farooqi, Benedict Paten, Mikhail Kolmogorov. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv 2024.03.22.24304756; doi: https://doi.org/10.1101/2024.03.22.24304756"
+  somalier:
+    citation: "Somalier (Pedersen et al. 2020)"
+    bibliography: "Pedersen, B.S., Bhetariya, P.J., Brown, J. et al. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Med 12, 62 (2020). https://doi.org/10.1186/s13073-020-00761-2"
+  split_bed_chunks:
+    citation: "split_bed_chunks"
+    bibliography: ""
+  splitubam:
+    citation: "splitubam"
+    bibliography: ""
+  stranger:
+    citation: "Stranger (Nilsson & Magnusson 2021)"
+    bibliography: "Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873"
+  svdb:
+    citation: "SVDB (Eisfeldt et al. 2017)"
+    bibliography: ""
+  tabix:
+    citation: "Tabix (Li 2011)"
+    bibliography: "Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011;27(5):718-719. doi:10.1093/bioinformatics/btq671"
+  trgt:
+    citation: "TRGT (Dolzhenko et al. 2024)"
+    bibliography: "Dolzhenko, E., English, A., Dashnow, H. et al. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02057-3"
+  untar:
+    citation: "untar"
+    bibliography: ""
+  yak:
+    citation: "yak"
+    bibliography: ""
+  whatshap:
+    citation: "WhatsHap (Martin et al. 2016)"
+    bibliography: "Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O Fischer, Nadia Pisanti, Gunnar W Klau, Alexander Schöenhuth, Tobias Marschall. bioRxiv 085050; doi: https://doi.org/10.1101/085050"
diff --git a/assets/svdb_query_vcf_schema.json b/assets/svdb_query_vcf_schema.json
new file mode 100644
index 00000000..a927a1f3
--- /dev/null
+++ b/assets/svdb_query_vcf_schema.json
@@ -0,0 +1,40 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json",
+    "title": "Schema for SVDB query - VCF",
+    "description": "Schema for the SVDB query database input, VCF version",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "filename": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+\\.vcf?(\\.gz)?$",
+                "errorMessage": "Path to query database cannot contain spaces and must be a vcf file"
+            },
+            "in_freq_info_key": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "In frequency key cannot contain spaces"
+            },
+            "in_allele_count_info_key": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "In allele count key cannot contain spaces"
+            },
+            "out_freq_info_key": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Out frequency key must be provided and cannot contain spaces"
+            },
+            "out_allele_count_info_key": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Out allele count key must be provided and cannot contain spaces"
+            }
+        },
+        "required": ["filename", "out_freq_info_key", "out_allele_count_info_key"]
+    }
+}
diff --git a/assets/vep_plugin_files_schema.json b/assets/vep_plugin_files_schema.json
index d904317b..e436840c 100644
--- a/assets/vep_plugin_files_schema.json
+++ b/assets/vep_plugin_files_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/vep_plugin_files_schema.json",
     "title": "Schema for VEP plugin files and their indices",
     "description": "Schema for VEP plugin files and their indices",
diff --git a/conf/base.config b/conf/base.config
index 2bc62420..04acaf56 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,9 +10,9 @@
 
 process {
 
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -23,36 +23,36 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
+    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withName: 'HIFIASM' {
-        time   = { check_max( 36.h  * task.attempt, 'time'    ) }
+        time   = { 36.h  * task.attempt }
     }
-
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }
@@ -60,8 +60,8 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-
-    withName: '.*:SAMTOOLS_MERGE' {
+    withName: 'SAMTOOLS_MERGE|SAMTOOLS_INDEX' {
         label = 'process_medium'
     }
+
 }
diff --git a/conf/modules/annotate_consequence_pli.config b/conf/modules/annotate_consequence_pli.config
index 3158c4f4..648c98e6 100644
--- a/conf/modules/annotate_consequence_pli.config
+++ b/conf/modules/annotate_consequence_pli.config
@@ -12,6 +12,10 @@
 */
 
 process {
+
+    //
+    // SNVs
+    //
     withName: '.*:ANN_CSQ_PLI_SNV:.*' {
         publishDir = [
             enabled: false
@@ -29,4 +33,25 @@ process {
     withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' {
         ext.prefix = { "${meta.id}_snv_csq_pli" }
     }
+
+    //
+    // SVs
+    //
+    withName: '.*:ANN_CSQ_PLI_SVS:.*' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:ADD_MOST_SEVERE_CSQ' {
+        ext.prefix = { "${meta.id}_svs_csq" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:ADD_MOST_SEVERE_PLI' {
+        ext.prefix = { "${meta.id}_svs_csq_pli" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:TABIX_BGZIPTABIX' {
+        ext.prefix = { "${meta.id}_svs_csq_pli" }
+    }
 }
diff --git a/conf/modules/annotate_repeat_expansions.config b/conf/modules/annotate_repeat_expansions.config
index 93538810..db1d0481 100644
--- a/conf/modules/annotate_repeat_expansions.config
+++ b/conf/modules/annotate_repeat_expansions.config
@@ -23,13 +23,13 @@ process {
     }
 
     withName: '.*:ANNOTATE_REPEAT_EXPANSIONS:COMPRESS_STRANGER' {
-        ext.prefix = { "${meta.id}_repeat_expansion_stranger" }
+        ext.prefix = { "${meta.id}_repeats_annotated" }
         ext.args   = [
             '--output-type z',
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/repeat_annotation/stranger/${meta.id}" },
+            path: { "${params.outdir}/repeats/family/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config
new file mode 100644
index 00000000..a3274a9f
--- /dev/null
+++ b/conf/modules/annotate_svs.config
@@ -0,0 +1,57 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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 {
+
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Annotate SVs
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
+    withName: '.*:ANNOTATE_SVS:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*ANNOTATE_SVS:ENSEMBLVEP_SV' {
+        ext.prefix = { params.skip_cnv_calling ? "${meta.id}_svs_merged_annotated" : "${meta.id}_svs_cnvs_merged_annotated" }
+        ext.args = { [
+            "${params.extra_vep_options}",
+            '--dir_plugins .',
+            '--plugin pLI,pLI_values.txt',
+            '--appris --biotype --buffer_size 100 --canonical --cache --ccds',
+            '--compress_output bgzip --distance 5000 --domains',
+            '--exclude_predicted --force_overwrite --format vcf',
+            '--hgvs --humdiv --max_sv_size 248387328',
+            '--no_progress --numbers --per_gene --polyphen p',
+            '--protein --offline --sift p --regulatory',
+            '--symbol --tsl --uniprot --vcf',
+            '--no_stats'
+        ].join(' ') }
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_rank_variants ? null : filename }
+        ]
+    }
+
+    withName: '.*ANNOTATE_SVS:TABIX_ENSEMBLVEP_SV' {
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_rank_variants ? null : filename }
+        ]
+    }
+
+}
diff --git a/conf/modules/assembly_variant_calling.config b/conf/modules/assembly_variant_calling.config
index acd8344b..c31206cd 100644
--- a/conf/modules/assembly_variant_calling.config
+++ b/conf/modules/assembly_variant_calling.config
@@ -19,9 +19,7 @@ process {
     }
 
     withName: '.*:ASSEMBLY_VARIANT_CALLING:DIPCALL' {
-
         ext.args = '--cs'
-
         publishDir = [
             path: { "${params.outdir}/assembly_variant_calling/dipcall/${meta.id}" },
             mode: params.publish_dir_mode,
diff --git a/conf/modules/bam_infer_sex.config b/conf/modules/bam_infer_sex.config
index d247a841..0cd27975 100644
--- a/conf/modules/bam_infer_sex.config
+++ b/conf/modules/bam_infer_sex.config
@@ -31,7 +31,7 @@ process {
     withName: '.*:BAM_INFER_SEX:RELATE_RELATE' {
         ext.args = '--infer'
         publishDir = [
-            path: { "${params.outdir}/qc_aligned_reads/somalier/relate/${meta.id}" },
+            path: { "${params.outdir}/qc/somalier/relate/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/modules/structural_variant_calling.config b/conf/modules/call_cnvs.config
similarity index 56%
rename from conf/modules/structural_variant_calling.config
rename to conf/modules/call_cnvs.config
index 8e1e5a28..9256907a 100644
--- a/conf/modules/structural_variant_calling.config
+++ b/conf/modules/call_cnvs.config
@@ -14,31 +14,46 @@ process {
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Structural variant calling
+    Call CNVs
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    withName: '.*:STRUCTURAL_VARIANT_CALLING:SNIFFLES' {
-
-        ext.prefix = { "${meta.id}_sniffles" }
-
-        ext.args = '--no-qc'
+    withName: '.*:CALL_CNVS:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
 
+    withName: '.*:CALL_CNVS:HIFICNV' {
+        ext.prefix = { "${meta.id}_hificnv" }
         publishDir = [
-            path: { "${params.outdir}/sv_calling/sniffles/single_sample/${meta.id}" },
+            path: { "${params.outdir}/visualization_tracks/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.endsWith('.bw') || filename.endsWith('.bedgraph') ? filename : null }
         ]
     }
 
-    withName: '.*:STRUCTURAL_VARIANT_CALLING:SNIFFLES_MULTISAMPLE' {
-
-        ext.prefix = { "${meta.id}_sniffles" }
-
+    withName: '.*:CALL_CNVS:ADD_FOUND_IN_TAG' {
+        ext.prefix = { "${meta.id}_cnvs" }
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type z',
+            '--write-index=tbi',
+            '--no-version'
+        ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/sv_calling/sniffles/multi_sample/${meta.id}" },
+            path: { "${params.outdir}/svs/sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: '.*:CALL_CNVS:SVDB_MERGE' {
+        ext.prefix = { "${meta.id}_cnvs_merged" }
+        ext.args = [
+            '--bnd_distance 10000',
+            '--overlap .5'
+        ].join(' ')
+    }
+
 }
diff --git a/conf/modules/call_paralogs.config b/conf/modules/call_paralogs.config
index a258a177..4ef63135 100644
--- a/conf/modules/call_paralogs.config
+++ b/conf/modules/call_paralogs.config
@@ -19,23 +19,11 @@ process {
     */
 
     withName: '.*:CALL_PARALOGS:PARAPHASE' {
-
+        ext.args = { "${params.extra_paraphase_options}" }
         publishDir = [
             path: { "${params.outdir}/paraphase/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.vcf') ? null : filename }
         ]
     }
-
-    withName: '.*:CALL_PARALOGS:TABIX_BGZIPTABIX' {
-
-        ext.prefix = { "${input.simpleName}" }
-
-        publishDir = [
-            path: { "${params.outdir}/paraphase/${meta.id}/${meta.id}_paraphase_vcfs" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
 }
diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config
index d46150df..43b2d1c9 100644
--- a/conf/modules/call_repeat_expansions.config
+++ b/conf/modules/call_repeat_expansions.config
@@ -24,14 +24,14 @@ process {
         ]
     }
 
-    withName: '.*:CALL_REPEAT_EXPANSIONS:TRGT' {
+    withName: '.*:CALL_REPEAT_EXPANSIONS:TRGT_GENOTYPE' {
         ext.args = { "--sample-name ${meta.id}" }
     }
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT_TRGT' {
         ext.prefix = { "${meta.id}_spanning_sorted" }
         publishDir = [
-            path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
+            path: { "${params.outdir}/repeats/sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -39,7 +39,7 @@ process {
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:SAMTOOLS_INDEX_TRGT' {
         publishDir = [
-            path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
+            path: { "${params.outdir}/repeats/sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -52,31 +52,33 @@ process {
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
+            path: { "${params.outdir}/repeats/sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_MERGE' {
+    withName: '.*:CALL_REPEAT_EXPANSIONS:TRGT_MERGE' {
+        ext.prefix = { "${meta.id}_repeats" }
         ext.args = [
             '--output-type z',
-            '--write-index=tbi',
             '--force-single'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/repeat_calling/trgt/multi_sample/${meta.id}" },
+            path: { "${params.outdir}/repeats/family/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_repeat_annotation ? null : filename }
         ]
     }
 
-    withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_INDEX_MERGE' {
-        ext.args = '--tbi'
+    withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_INDEX' {
+        ext.prefix = { "${meta.id}_repeats" }
+        ext.args = "--tbi"
         publishDir = [
-            path: { "${params.outdir}/repeat_calling/trgt/multi_sample/${meta.id}" },
+            path: { "${params.outdir}/repeats/family/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_repeat_annotation ? null : filename }
         ]
     }
+
 }
diff --git a/conf/modules/call_svs.config b/conf/modules/call_svs.config
new file mode 100644
index 00000000..2969b1ff
--- /dev/null
+++ b/conf/modules/call_svs.config
@@ -0,0 +1,83 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Call SVs
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
+    withName: '.*:CALL_SVS:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*:CALL_SVS:ADD_FOUND_IN_TAG' {
+        ext.prefix = { "${meta.id}_found_in" }
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type b',
+            '--write-index=csi',
+            '--no-version'
+        ].join(' ')
+    }
+
+    withName: '.*:CALL_SVS:BCFTOOLS_QUERY' {
+        ext.args = '--list-samples'
+    }
+
+    withName: '.*:CALL_SVS:CREATE_SAMPLES_FILE' {
+        ext.prefix = { "${meta.id}_samples_file" }
+    }
+
+    withName: '.*:CALL_SVS:SNIFFLES' {
+        ext.prefix = { "${meta.id}_sniffles_for_reheader" }
+        ext.args = '--no-qc'
+    }
+
+    withName: '.*:CALL_SVS:SVDB_MERGE' {
+        ext.prefix = { "${meta.id}_svs_merged" }
+        ext.args = [
+            '--bnd_distance 1000',
+            '--overlap .5'
+        ].join(' ')
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_sv_annotation || !params.skip_cnv_calling ? null : filename }
+        ]
+    }
+
+    withName: '.*:CALL_SVS:TABIX_SVDB_MERGE' {
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_sv_annotation || !params.skip_cnv_calling ? null : filename }
+        ]
+    }
+
+    withName: '.*:CALL_SVS:BCFTOOLS_REHEADER' {
+        ext.prefix = { "${meta.id}_svs" }
+        ext.args2 = [
+            '--output-type z',
+            '--write-index=tbi'
+        ].join(' ')
+        publishDir = [
+            path: { "${params.outdir}/svs/sample/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
diff --git a/conf/modules/cnv.config b/conf/modules/cnv.config
deleted file mode 100644
index e11c3553..00000000
--- a/conf/modules/cnv.config
+++ /dev/null
@@ -1,36 +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 {
-
-    /*
-    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CNV
-    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    */
-
-    withName: '.*:CNV:HIFICNV' {
-        publishDir = [
-            path: { "${params.outdir}/cnv_calling/hificnv/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:CNV:TABIX_HIFICNV' {
-        publishDir = [
-            path: { "${params.outdir}/cnv_calling/hificnv/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/conf/modules/filter_variants.config b/conf/modules/filter_variants.config
new file mode 100644
index 00000000..be030953
--- /dev/null
+++ b/conf/modules/filter_variants.config
@@ -0,0 +1,77 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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 {
+
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Filter variants
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
+    withName: '.*:FILTER_VARIANTS_SNV:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*:FILTER_VARIANTS_SNVS:ENSEMBLVEP_FILTERVEP' {
+        ext.args   = { "--filter \"HGNC_ID in ${feature_file}\"" }
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*:FILTER_VARIANTS_SVS:ENSEMBLVEP_FILTERVEP' {
+        ext.args   = { "--filter \"HGNC_ID in ${feature_file}\"" }
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
+    withName: '.*:FILTER_VARIANTS_SNVS:BCFTOOLS_VIEW' {
+        ext.prefix = { params.skip_snv_annotation ? "${meta.id}_snvs_filtered" : (params.skip_rank_variants ? "${meta.id}_snvs_annotated_filtered" : "${meta.id}_snvs_annotated_ranked_filtered") }
+        ext.args   = { [
+            '--output-type z',
+            '--write-index=tbi',
+            "${params.filter_snvs_expression}"
+        ].join(" ") }
+        publishDir = [
+            path: { "${params.outdir}/snvs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*:FILTER_VARIANTS_SVS:BCFTOOLS_VIEW' {
+        ext.prefix = {
+            def parts = []
+            parts << "${meta.id}"
+            parts << (params.skip_cnv_calling ? 'svs_merged' : 'svs_cnvs_merged')
+            if (!params.skip_sv_annotation) parts << 'annotated'
+            if (!params.skip_rank_variants) parts << 'ranked'
+            parts << 'filtered'
+            return parts.join('_')
+        }
+        ext.args   = { [
+            '--output-type z',
+            '--write-index=tbi',
+            "${params.filter_svs_expression}"
+        ].join(" ") }
+                publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+}
diff --git a/conf/modules/general.config b/conf/modules/general.config
index b1aee9ae..1980639b 100644
--- a/conf/modules/general.config
+++ b/conf/modules/general.config
@@ -27,34 +27,44 @@ process {
     withName: '.*:NALLO:BCFTOOLS_STATS' {
         ext.prefix = { "${vcf}" }
         publishDir = [
-            path: { "${params.outdir}/snvs/stats/single_sample" },
+            path: { "${params.outdir}/snvs/stats/sample" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: '.*:NALLO:BCFTOOLS_CONCAT' {
-        ext.prefix = { params.skip_snv_annotation ? "${meta.id}_snv" : (params.skip_rank_variants ? "${meta.id}_snv_annotated" : "${meta.id}_snv_annotated_ranked") }
+        ext.prefix = { "${meta.id}_concat" }
         ext.args = { [
             '--allow-overlaps',
+            '--output-type u'
+        ].join(' ') }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:NALLO:BCFTOOLS_SORT' {
+        ext.prefix = { params.skip_snv_annotation ? "${meta.id}_snv" : (params.skip_rank_variants ? "${meta.id}_snv_annotated" : "${meta.id}_snv_annotated_ranked") }
+        ext.args = { [
             '--output-type z',
             '--write-index=tbi'
         ].join(' ') }
         publishDir = [
-            path: { "${params.outdir}/snvs/multi_sample/${meta.id}" },
+            path: { "${params.outdir}/snvs/family/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT' {
+    withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT_SNVS' {
         ext.args = [
             '-i \'GT="alt"\'',
             '--output-type z',
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/snvs/single_sample/" },
+            path: { "${params.outdir}/snvs/sample/" },
             mode: params.publish_dir_mode,
             // Can't use prefix as it would come from the original file
             saveAs: { filename ->
@@ -65,32 +75,33 @@ process {
                     def sample = matcher[0][1]
                     def extension = matcher[0][2]
                     def annotated = params.skip_snv_annotation ? "" : (params.skip_rank_variants ? "_annotated" : "_annotated_ranked" )
-                    "${sample}/${sample}_snv${annotated}${extension}"
+                    "${sample}/${sample}_snvs${annotated}${extension}"
                 }
             }
         ]
     }
-    withName: '.*:NALLO:FASTQC' {
-        ext.args = '--quiet'
-        publishDir = [
-            path: { "${params.outdir}/qc_raw_reads/fastqc/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 
-    withName: '.*:NALLO:FQCRS' {
-        ext.prefix = { "${reads}" }
+    withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT_SVS' {
+        ext.args = [
+            '-i \'GT="alt"\'',
+            '--output-type z',
+            '--write-index=tbi'
+        ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/qc_raw_reads/fqcrs/${meta.id}" },
+            path: { "${params.outdir}/svs/sample/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:NALLO:CAT_FASTQ' {
-        publishDir = [
-            enabled: false
+            // Can't use prefix as it would come from the original file
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) {
+                    null
+                } else {
+                    def matcher = filename =~ /(.+)(\.vcf\.gz(?:\.tbi)?)$/
+                    def sample = matcher[0][1]
+                    def extension = matcher[0][2]
+                    def annotated = params.skip_sv_annotation ? "" : "_annotated"
+                    "${sample}/${sample}_svs${annotated}${extension}"
+                }
+            }
         ]
     }
 
@@ -100,9 +111,9 @@ process {
         ]
     }
 
-    withName: '.*:NALLO:SOMALIER_PED' {
+    withName: '.*:NALLO:SOMALIER_PED_FAMILY' {
         publishDir = [
-            path: { "${params.outdir}/pedigree" },
+            path: { "${params.outdir}/pedigree/family/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
@@ -120,34 +131,37 @@ process {
     }
 
     withName: '.*:NALLO:SPLITUBAM' {
-        ext.args = { "--split ${params.parallel_alignments}" }
+        ext.args = { "--split ${params.alignment_processes}" }
         publishDir = [
             enabled: false
         ]
     }
 
     withName: '.*:NALLO:MINIMAP2_ALIGN' {
-        ext.prefix = { "${meta.id}_aligned" }
+        // Samtools will not sort supplementary reads properly, to snapshot the md5sum
+        // they must be input in the same order and can therefore not be named the same
+        ext.prefix = { meta.n_files > 1 ? "${reads}" : "${meta.id}_aligned}" }
         ext.args = { [
             "-y",
-            params.preset.equals('ONT_R10') ? "-x lr:hq" : "-x map-hifi",
+            "-x ${params.minimap2_read_mapping_preset}",
             "--secondary=no",
             "-Y",
             "-R @RG\\\\tID:${meta.id}\\\\tSM:${meta.id}"
         ].join(' ') }
         ext.args3 = { [
             '-x HP,PS', // phasing
-            '-x AS,CC,CG,CP,H1,H2,HI,H0,IH,MC,MD,MQ,NM,SA,TS'
+            '-x AS,CC,CG,CP,H1,H2,HI,H0,IH,MC,MD,MQ,NM,SA,TS',
+            '--no-RG' // read group information
         ].join(' ') }
         ext.args4 = '-T \\*'
         publishDir = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/aligned_reads/${meta.id}" },
-                // only a single BAM file per sample
-                saveAs: { filename ->
-                    filename.equals('versions.yml') ? null : (meta.n_files == 1 && params.skip_phasing_wf ? filename : null)
-                }
-            ]
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/aligned_reads/${meta.id}" },
+            // A BAM file is only published from here if no merging is required (a sample with one input file), and if phasing is off
+            saveAs: { filename ->
+                filename.equals('versions.yml') ? null : (meta.n_files == 1 && params.skip_phasing ? filename : null)
+            }
+        ]
     }
 
     withName: '.*:NALLO:SAMTOOLS_MERGE' {
@@ -156,15 +170,24 @@ process {
         publishDir = [
             path: { "${params.outdir}/aligned_reads/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : (params.skip_phasing_wf ? filename : null) }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : (params.skip_phasing ? filename : null) }
         ]
     }
 
-    withName: '.*:NALLO:ECHTVAR_ENCODE' {
+    withName: '.*:NALLO:SVDB_MERGE_SVS_CNVS' {
+        ext.prefix = { "${meta.id}_svs_cnvs_merged" }
         publishDir = [
-            path: { "${params.outdir}/databases/echtvar/encode/${meta.id}" },
+            path: { "${params.outdir}/svs/family/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_sv_annotation ? null : filename }
+        ]
+    }
+
+    withName: '.*:NALLO:TABIX_SVDB_MERGE_SVS_CNVS' {
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_sv_annotation ? null : filename }
         ]
     }
 
diff --git a/conf/modules/genome_assembly.config b/conf/modules/genome_assembly.config
index 761f1eb0..4c2e91a4 100644
--- a/conf/modules/genome_assembly.config
+++ b/conf/modules/genome_assembly.config
@@ -24,29 +24,34 @@ process {
         ]
     }
 
-    withName: '.*:ASSEMBLY:YAK_PATERNAL' {
+    withName: '.*:ASSEMBLY:HIFIASM' {
+        ext.args = { [
+            "${params.extra_hifiasm_options}",
+            '--dual-scaf',
+            '--telo-m CCCTAA'
+        ].join(' ') }
+        publishDir = [
+            enabled: false,
+        ]
+    }
 
+    withName: '.*:ASSEMBLY:YAK_PATERNAL' {
         ext.prefix = { "${meta.paternal_id}_yak" }
-
         publishDir = [
             enabled: false,
         ]
     }
 
     withName: '.*:ASSEMBLY:YAK_MATERNAL' {
-
         ext.prefix = { "${meta.maternal_id}_yak" }
-
         publishDir = [
             enabled: false,
         ]
     }
 
     withName: '.*:ASSEMBLY:GFASTATS.*' {
-
         ext.args = '--discover-paths'
         ext.prefix = { "${assembly.baseName}" }
-
         publishDir = [
             path: { "${params.outdir}/assembly_haplotypes/gfastats/${meta.id}" },
             mode: params.publish_dir_mode,
diff --git a/conf/modules/methylation.config b/conf/modules/methylation.config
index 2101bd30..188842a7 100644
--- a/conf/modules/methylation.config
+++ b/conf/modules/methylation.config
@@ -24,48 +24,27 @@ process {
         ]
     }
 
-    withName: '.*:METHYLATION:MODKIT_PILEUP_UNPHASED' {
-
-        ext.args = '--combine-mods --cpg --combine-strands'
+    withName: '.*:METHYLATION:MODKIT_PILEUP' {
+        ext.args = { [
+            "${params.extra_modkit_options}",
+            '--combine-mods',
+            '--cpg',
+            '--combine-strands',
+            !params.skip_phasing ? '--partition-tag HP' : '',
+        ].join(' ') }
         ext.prefix = { "${meta.id}_modkit_pileup" }
-
         publishDir = [
-            path: { "${params.outdir}/methylation/modkit/pileup/unphased/${meta.id}" },
+            path: { "${params.outdir}/methylation/modkit/pileup/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.endsWith('.log') ? filename : null }
         ]
     }
 
-    withName: '.*:METHYLATION:MODKIT_PILEUP_PHASED' {
-
-        ext.args = '--combine-mods --cpg --combine-strands --partition-tag HP'
-        ext.prefix = { "${meta.id}_modkit_pileup_phased" }
-
-        publishDir = [
-            path: { "${params.outdir}/methylation/modkit/pileup/phased/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.endsWith('.log') ? filename : null }
-        ]
-
-    }
-
-    withName: '.*:METHYLATION:BGZIP_MODKIT_PILEUP_UNPHASED' {
 
+    withName: '.*:METHYLATION:TABIX_BGZIPTABIX' {
         ext.prefix = { "${input.simpleName}" }
-
-        publishDir = [
-            path: { "${params.outdir}/methylation/modkit/pileup/unphased/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:METHYLATION:BGZIP_MODKIT_PILEUP_PHASED' {
-
-        ext.prefix = { "${input.simpleName}" }
-
         publishDir = [
-            path: { "${params.outdir}/methylation/modkit/pileup/phased/${meta.id}" },
+            path: { "${params.outdir}/methylation/modkit/pileup/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/modules/phasing.config b/conf/modules/phasing.config
index e747b420..80cec5d5 100644
--- a/conf/modules/phasing.config
+++ b/conf/modules/phasing.config
@@ -24,34 +24,48 @@ process {
         ]
     }
 
-    withName: '.*:PHASING:HIPHASE_SNV' {
-        ext.prefix = { "$meta.id}_phased" }
+    withName: '.*:PHASING:HIPHASE' {
         ext.args = { [
             '--ignore-read-groups',
             "--stats-file ${meta.id}_phased.stats.tsv",
             "--blocks-file ${meta.id}_phased.blocks.tsv",
             "--summary-file ${meta.id}_phased.summary.tsv"
         ].join(' ') }
-
         publishDir = [
             path: { "${params.outdir}/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : ((filename.endsWith('bam') || filename.endsWith('bai')) ? "aligned_reads/${meta.id}/${filename}" : "phasing/hiphase/snv/${meta.id}/${filename}" ) }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : ((filename.endsWith('bam') || filename.endsWith('bai')) ? "aligned_reads/${meta.id}/${filename}" : "phased_variants/${meta.id}/${filename}" ) }
         ]
     }
 
-    withName: '.*:PHASING:HIPHASE_SV' {
-        ext.prefix = { "$meta.id}_phased" }
-        ext.args = { [
-            '--ignore-read-groups',
-            "--stats-file ${meta.id}_phased.stats.tsv",
-            "--blocks-file ${meta.id}_phased.blocks.tsv",
-            "--summary-file ${meta.id}_phased.summary.tsv"
-        ].join(' ') }
+    withName: '.*:PHASING:LONGPHASE_PHASE' {
+        ext.prefix = { "${meta.id}_phased" }
+        ext.args = [
+            params.preset.equals('ONT_R10') ? "--ont" : "--pb",
+            '--indels'
+        ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/" },
+            path: { "${params.outdir}/phased_variants/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : ((filename.endsWith('bam') || filename.endsWith('bai')) ? "aligned_reads/${meta.id}/${filename}" : "phasing/hiphase/sv/${meta.id}/${filename}" ) }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*:PHASING:TABIX_LONGPHASE_PHASE' {
+        publishDir = [
+            path: { "${params.outdir}/phased_variants/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+
+    withName: '.*:PHASING:LONGPHASE_HAPLOTAG' {
+        ext.prefix = { "${meta.id}_haplotagged" }
+        publishDir = [
+            path: { "${params.outdir}/aligned_reads/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -59,10 +73,11 @@ process {
         ext.prefix = { "${meta.id}_phased" }
         ext.args = [
             '--ignore-read-groups',
-            '--indels'
+            '--indels',
+            '--use-supplementary'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/phasing/whatshap/phase/${meta.id}" },
+            path: { "${params.outdir}/phased_variants/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -71,14 +86,14 @@ process {
     withName: '.*:PHASING:WHATSHAP_STATS' {
         ext.prefix = { "${meta.id}_stats" }
         publishDir = [
-            path: { "${params.outdir}/phasing/whatshap/stats/${meta.id}" },
+            path: { "${params.outdir}/qc/phasing_stats/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: '.*:PHASING:WHATSHAP_HAPLOTAG' {
-        ext.prefix = { "${meta.id}_phased" }
+        ext.prefix = { "${meta.id}_haplotagged" }
         ext.args = [
             '--ignore-read-groups',
             '--tag-supplementary'
@@ -90,7 +105,7 @@ process {
         ]
     }
 
-    withName: '.*:PHASING:SAMTOOLS_INDEX_WHATSHAP' {
+    withName: '.*:PHASING:SAMTOOLS_INDEX_WHATSHAP|.*:PHASING:SAMTOOLS_INDEX_LONGPHASE' {
         publishDir = [
             path: { "${params.outdir}/aligned_reads/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -105,7 +120,7 @@ process {
         ].join(' ')
         ext.prefix = { "${meta.id}_cramino_aligned_phased" }
         publishDir = [
-            path: { "${params.outdir}/qc_aligned_reads/cramino/phased/${meta.id}" },
+            path: { "${params.outdir}/qc/cramino/phased/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/modules/prepare_genome.config b/conf/modules/prepare_genome.config
index 412d7b75..62ee761a 100644
--- a/conf/modules/prepare_genome.config
+++ b/conf/modules/prepare_genome.config
@@ -19,11 +19,7 @@ process {
     }
 
     withName: '.*:PREPARE_GENOME:MINIMAP2_INDEX' {
-        if(params.preset == 'revio' | params.preset == 'pacbio') {
-            ext.args = "-x map-hifi"
-        } else if(params.preset == 'ONT_R9' | params.preset == 'ONT_R10') {
-            ext.args = "-x map-ont"
-        }
+        ext.args = { "-x ${params.minimap2_read_mapping_preset}" }
     }
 
     withName: '.*:PREPARE_GENOME:MINIMAP2_INDEX_DIPCALL' {
@@ -32,5 +28,6 @@ process {
 
     withName: '.*:PREPARE_GENOME:UNTAR_VEP_CACHE' {
         ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) }
+        ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' }
     }
 }
diff --git a/conf/modules/qc_aligned_reads.config b/conf/modules/qc_aligned_reads.config
index dda307bb..fd3746bb 100644
--- a/conf/modules/qc_aligned_reads.config
+++ b/conf/modules/qc_aligned_reads.config
@@ -22,7 +22,16 @@ process {
         ext.args = '--karyotype'
         ext.prefix = { "${meta.id}_cramino_aligned" }
         publishDir = [
-            path: { "${params.outdir}/qc_aligned_reads/cramino/unphased/${meta.id}" },
+            path: { "${params.outdir}/qc/cramino/unphased/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*:QC_ALIGNED_READS:FASTQC' {
+        ext.args = '--quiet --format bam'
+        publishDir = [
+            path: { "${params.outdir}/qc/fastqc/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -32,10 +41,10 @@ process {
         ext.args = { [
             '--fast-mode',
             '--no-per-base',
-            params.bed ? '' : '--by 500'
+            params.target_regions ? '' : '--by 500'
         ].join(' ') }
         publishDir = [
-            path: { "${params.outdir}/qc_aligned_reads/mosdepth/${meta.id}" },
+            path: { "${params.outdir}/qc/mosdepth/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config
index d253ffa2..26be17dc 100644
--- a/conf/modules/rank_variants.config
+++ b/conf/modules/rank_variants.config
@@ -11,18 +11,16 @@
 ----------------------------------------------------------------------------------------
 */
 
-//
-// Score and rank SNVs
-//
-
 process {
 
+    //
+    // Score and rank SNVs
+    //
     withName: '.*:RANK_VARIANTS_SNV:.*' {
         publishDir = [
             enabled: false,
         ]
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_ANNOTATE' {
         ext.prefix = { "${meta.id}_snv_genmod_annotate" }
         ext.args = { [
@@ -31,24 +29,66 @@ process {
             '--temp_dir ./'
             ].join(' ') }
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_MODELS' {
         ext.prefix = { "${meta.id}_snv_genmod_models" }
         ext.args = "--whole_gene --temp_dir ./"
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_SCORE' {
         ext.prefix = { "${meta.id}_snv_genmod_score" }
         ext.args = "--rank_results"
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_COMPOUND' {
         ext.prefix = { "${meta.id}_snv_genmod_compound" }
         ext.args = "--temp_dir ./"
     }
-
     withName: '.*:RANK_VARIANTS_SNV:BCFTOOLS_SORT' {
-        ext.when = false
+        ext.prefix = { "${meta.id}_snv_genmod_compound_sorted" }
+        ext.args = [
+            '--output-type z',
+            '--write-index=tbi',
+            '--max-mem 6G'
+        ].join(' ')
     }
 
+    //
+    // Score and rank SVSs
+    //
+    withName: '.*:RANK_VARIANTS_SVS:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_ANNOTATE' {
+        ext.prefix = { "${meta.id}_svs_genmod_annotate" }
+        ext.args = { [
+            '--annotate_regions',
+            '--genome-build 38',
+            '--temp_dir ./'
+            ].join(' ') }
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_MODELS' {
+        ext.prefix = { "${meta.id}_svs_genmod_models" }
+        ext.args = '--whole_gene --temp_dir ./'
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_SCORE' {
+        ext.prefix = { "${meta.id}_svs_genmod_score" }
+        ext.args = '--rank_results'
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_COMPOUND' {
+        ext.prefix = { "${meta.id}_svs_genmod_compound" }
+        ext.args = '--temp_dir ./'
+    }
+    withName: '.*:RANK_VARIANTS_SVS:BCFTOOLS_SORT' {
+        ext.prefix = { params.skip_cnv_calling ? "${meta.id}_svs_merged_annotated_ranked" : "${meta.id}_svs_cnvs_merged_annotated_ranked" }
+        ext.args = [
+            '--output-type z',
+            '--write-index=tbi',
+            '--max-mem 6G'
+        ].join(' ')
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }
diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
index 2559d947..1975d044 100644
--- a/conf/modules/short_variant_calling.config
+++ b/conf/modules/short_variant_calling.config
@@ -24,7 +24,17 @@ process {
         ]
     }
 
-    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT' {
+    withName: '.*:SHORT_VARIANT_CALLING:ADD_FOUND_IN_TAG' {
+        ext.prefix = { "${meta.id}_found_in" }
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type b',
+            '--no-version'
+        ].join(' ')
+    }
+
+
+    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
         ext.args = { [
             "--sample_name=${meta.id}",
@@ -33,6 +43,14 @@ process {
             meta.sex == 1 ? '--haploid_contigs="chrX,chrY"' : ''
         ].join(' ') }
     }
+    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_VCFSTATSREPORT' {
+        publishDir = [
+            path: { "${params.outdir}/qc/deepvariant_vcfstatsreport/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+
+    }
 
     withName: '.*:SHORT_VARIANT_CALLING:GLNEXUS' {
         ext.args = '--config DeepVariant_unfiltered'
@@ -47,7 +65,8 @@ process {
         ext.args = [
             '-m -',
             '-w 10000',
-            '--output-type u',
+            '--output-type z',
+            '--write-index=tbi'
         ].join(' ')
     }
 
@@ -64,4 +83,5 @@ process {
             '-w 10000'
         ].join(' ')
     }
+
 }
diff --git a/conf/modules/snv_annotation.config b/conf/modules/snv_annotation.config
index 36be4406..01ae9f94 100644
--- a/conf/modules/snv_annotation.config
+++ b/conf/modules/snv_annotation.config
@@ -36,12 +36,13 @@ process {
         ].join(' ')
     }
 
-    withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_VEP' {
+    withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_SNV' {
         ext.prefix = { "${meta.id}_vep" }
         ext.args = { [
-            "--dir_plugins .",
-            "--plugin LoFtool,LoFtool_scores.txt",
-            "--plugin pLI,pLI_values.txt",
+            "${params.extra_vep_options}",
+            '--dir_plugins .',
+            '--plugin LoFtool,LoFtool_scores.txt',
+            '--plugin pLI,pLI_values.txt',
             '--distance 5000',
             '--buffer_size 20000',
             '--format vcf --max_sv_size 248387328',
diff --git a/conf/test.config b/conf/test.config
index a348f829..ec51373c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -9,96 +9,82 @@
 
 ----------------------------------------------------------------------------------------
 */
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 4
-    max_memory = '15.GB'
-    max_time   = '6.h'
-
-    // Input data
-
-    // Genome references
-
-    fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
-    input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
-
-    bed = params.pipelines_testdata_base_path + 'reference/test_data.bed'
-
-    // HiFiCNV
-    hificnv_xy      = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
-    hificnv_xx      = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
-    hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed'
-
-    // Dipcall
-    par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
-
-    // Repeats
-    trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
-    variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
-
-    // SNV Annotation
-    vep_cache        = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
-    vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
-    snp_db           = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
-
-    // Rank variants
-    reduced_penetrance       = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
-    score_config_snv         = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
-    variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
-
-    // Somalier
-    somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
-
-    parallel_snv = 2 // Create 2 parallel DeepVariant processes
-    preset = "revio"
-
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+
+    // Base directory for genomic-medicine-sweden/nallo test data
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
+
+    // References
+    fasta                     = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
+    input                     = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
+    target_regions            = params.pipelines_testdata_base_path + 'reference/test_data.bed'
+    filter_variants_hgnc_ids  = params.pipelines_testdata_base_path + 'testdata/hgnc_ids.tsv'
+    hificnv_expected_xy_cn    = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
+    hificnv_expected_xx_cn    = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
+    hificnv_excluded_regions  = params.pipelines_testdata_base_path + 'reference/empty.bed'
+    par_regions               = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
+    trgt_repeats              = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
+    stranger_repeat_catalog   = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
+    vep_cache                 = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
+    vep_plugin_files          = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
+    echtvar_snv_databases     = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
+    svdb_sv_databases         = params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv'
+    genmod_reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
+    genmod_score_config_snvs  = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
+    genmod_score_config_svs   = params.pipelines_testdata_base_path + 'reference/rank_model_svs.ini'
+    variant_consequences_snvs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
+    variant_consequences_svs  = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
+    somalier_sites            = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
+
+    // Pipeline options
+    alignment_processes       = 2
+    snv_calling_processes     = 2
+    preset                    = "revio"
+
+    // Test config options
+    extra_modkit_options      = '--seed 1 --sampling-frac 0.1'
+    extra_vep_options         = '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz'
+    extra_paraphase_options   = '--gene hba'
+    extra_hifiasm_options     = '-f0 -k30 -w30 -D10 -r1 -N1'
 }
 
-process {
-    withName: '.*:NALLO:ASSEMBLY:HIFIASM' {
-        ext.args = '-f0 -k30 -w30 -D10 -r1 -N1'
-    }
+// Impose same minimum Nextflow version as in nextflow.config
+manifest {
+    nextflowVersion = '!>=24.04.2'
+}
 
-    withName: '.*:CALL_PARALOGS:PARAPHASE' {
-        ext.args = '--gene hba'
-    }
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }
 
-    withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_VEP' {
-        ext.prefix = { "${meta.id}_vep" }
-        ext.args = { [
-            "--dir_plugins .",
-            "--plugin LoFtool,LoFtool_scores.txt",
-            "--plugin pLI,pLI_values.txt",
-            "--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz",
-            '--distance 5000',
-            '--buffer_size 20000',
-            '--format vcf --max_sv_size 248387328',
-            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
-            '--domains --exclude_predicted --force_overwrite',
-            '--hgvs --humdiv --no_progress --numbers',
-            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
-            '--uniprot --vcf',
-            '--no_stats'
-        ].join(' ') }
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    withLabel: 'process_high' {
+        cpus = 4
+        memory = '15.GB'
     }
-
-    withName: '.*:NALLO:PHASING:WHATSHAP_PHASE' {
-        ext.args = '--ignore-read-groups --indels --distrust-genotypes --include-homozygous'
+    withLabel: 'process_medium' {
+        cpus = 2
+        memory = '7.GB'
     }
-
-    withName: 'FASTQC|MINIMAP2_INDEX_DIPCALL|PARAPHASE|SNIFFLES|GFASTATS_PATERNAL|GFASTATS_MATERNAL|HIFICNV' {
+    withLabel: 'process_low' {
         cpus = 1
+        memory = '3.GB'
     }
-
-    withName: 'MINIMAP2_INDEX|HIFIASM' {
-        cpus = 2
-    }
-
-    withName: 'SAMTOOLS_FASTQ|FASTP|MINIMAP2_ALIGN|GLNEXUS|ENSEMBLVEP_VEP|MODKIT_PILEUP|MODKIT_PILEUP_HAPLOTYPES' {
-        cpus = 4
+    withLabel: 'process_single' {
+        cpus = 1
+        memory = '3.GB'
     }
-
 }
diff --git a/CITATIONS.md b/docs/CITATIONS.md
similarity index 88%
rename from CITATIONS.md
rename to docs/CITATIONS.md
index 811889b7..5128c352 100644
--- a/CITATIONS.md
+++ b/docs/CITATIONS.md
@@ -48,8 +48,6 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
-- [fqcrs](https://github.com/fellen31/fqcrs)
-
 - [Genmod](https://github.com/Clinical-Genomics/genmod)
 
   > Magnusson M, Hughes T, Glabilloy, Bitdeli Chef. genmod: Version 3.7.3. Published online November 15, 2018. doi:10.5281/ZENODO.3841142
@@ -72,6 +70,10 @@
 
 - [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)
 
+- [LongPhase](https://github.com/twolinin/longphase)
+
+  > Jyun-Hong Lin, Liang-Chi Chen, Shu-Chi Yu, Yao-Ting Huang, LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants, Bioinformatics, Volume 38, Issue 7, March 2022, Pages 1816–1822, https://doi.org/10.1093/bioinformatics/btac058
+
 - [minimap2](https://academic.oup.com/bioinformatics/article/34/18/3094/4994778)
 
   > Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191
@@ -90,6 +92,10 @@
 
   > Genome-wide profiling of highly similar paralogous genes using HiFi sequencing. Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M Devaney, Jessica Noya, April S Berlyoung, Rhonda Brandon, Kathleen S Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, UCI Genomics Research to Elucidate the Genetics of Rare Diseases (UCI GREGoR) Consortium, Michael A Eberle. bioRxiv 2024.04.19.590294; doi: https://doi.org/10.1101/2024.04.19.590294
 
+- [Severus](https://www.medrxiv.org/content/10.1101/2024.03.22.24304756v1)
+
+  > Ayse Keskus, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky, Ataberk Donmez, Lisa A. Lansdon, Isabel Rodriguez, Jimin Park, Yuelin Liu, Xiwen Cui, Joshua Gardner, Brandy McNulty, Samuel Sacco, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Daniel E. Cook, Pi-Chuan Chang, Alexey Kolesnikov, Andrew Carroll, Erin K. Molloy, Irina Pushel, Erin Guest, Tomi Pastinen, Kishwar Shafin, Karen H. Miga, Salem Malikic, Chi-Ping Day, Nicolas Robine, Cenk Sahinalp, Michael Dean, Midhat S. Farooqi, Benedict Paten, Mikhail Kolmogorov. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv 2024.03.22.24304756; doi: https://doi.org/10.1101/2024.03.22.24304756
+
 - [Sniffles2](https://www.nature.com/articles/s41587-023-02024-y)
 
   > Smolka, M., Paulin, L.F., Grochowski, C.M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02024-y
@@ -104,6 +110,10 @@
 
   > Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873
 
+- [SVDB](https://github.com/J35P312/SVDB)
+
+  > Eisfeldt et al., 2017.
+
 - [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)
 
   > Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011;27(5):718-719. doi:10.1093/bioinformatics/btq671
diff --git a/docs/images/nallo_metromap.png b/docs/images/nallo_metromap.png
new file mode 100644
index 00000000..26804f76
Binary files /dev/null and b/docs/images/nallo_metromap.png differ
diff --git a/docs/images/nallo_metromap.svgz b/docs/images/nallo_metromap.svgz
new file mode 100644
index 00000000..9ddd168a
Binary files /dev/null and b/docs/images/nallo_metromap.svgz differ
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..a51e039b
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,114 @@
+---
+title: genomic-medicine-sweden/nallo
+description: A bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease.
+---
+
+## Introduction
+
+**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf).
+
+<picture align="center">
+    <img alt="genomic-medicine-sweden/nallo workflow" src="images/nallo_metromap.png">
+  </picture>
+
+## Pipeline summary
+
+### QC
+
+- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino) and [mosdepth](https://github.com/brentp/mosdepth)
+
+### Alignment & assembly
+
+- Align reads to reference with [minimap2](https://github.com/lh3/minimap2)
+- Assemble (trio-binned) haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm) (HiFi only)
+
+### Variant calling
+
+- Call SNVs & joint genotyping with [deepvariant](https://github.com/google/deepvariant) and [GLNexus](https://github.com/dnanexus-rnd/GLnexus)
+- Call SVs with [Severus](https://github.com/KolmogorovLab/Severus) or [Sniffles2](https://github.com/fritzsedlazeck/Sniffles)
+- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)
+- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only)
+- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase)
+- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall) (HiFi only)
+
+### Phasing and methylation
+
+- Phase and haplotag reads with [LongPhase](https://github.com/twolinin/longphase), [whatshap](https://github.com/whatshap/whatshap) or [HiPhase](https://github.com/PacificBiosciences/HiPhase)
+- Create methylation pileups with [modkit](https://github.com/nanoporetech/modkit)
+
+### Annotation
+
+- Annotate SNVs and INDELs with databases of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep)
+- Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger)
+- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep)
+
+### Ranking
+
+- Rank SNVs, INDELs, SVs and CNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)
+
+### Filtering
+
+- Filter SNVs, INDELs, SVs and CNVs with [filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html)
+
+## 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.
+
+Prepare a samplesheet with input data:
+
+`samplesheet.csv`
+
+```
+project,sample,file,family_id,paternal_id,maternal_id,sex,phenotype
+NIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2
+NIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1
+```
+
+Supply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using:
+
+```bash
+nextflow run genomic-medicine-sweden/nallo \
+    -profile <docker/singularity/.../institute> \
+    --input samplesheet.csv \
+    --preset <revio/pacbio/ONT_R10> \
+    --fasta <reference.fasta> \
+    --outdir <OUTDIR>
+```
+
+!!!warning
+
+    Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+
+To run in an offline environment, download the pipeline and singularity images using [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use):
+
+```
+nf-core download genomic-medicine-sweden/nallo
+```
+
+For more details and further functionality, please refer to the [usage documentation](usage.md).
+
+## Credits
+
+genomic-medicine-sweden/nallo was originally written by Felix Lenner.
+
+We thank the following people for their extensive assistance in the development of this pipeline:
+
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the [contributing guidelines](https://github.com/genomic-medicine-sweden/nallo/blob/dev/.github/CONTRIBUTING.md).
+
+## Citations
+
+If you use genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.13748210](https://doi.org/10.5281/zenodo.13748210).
+
+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/main/LICENSE).
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
diff --git a/docs/output.md b/docs/output.md
index b0e86626..f8450ee2 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,354 +1,283 @@
 # genomic-medicine-sweden/nallo: Output
 
-## Table of contents
-
-- [genomic-medicine-sweden/nallo: Output](#genomic-medicine-swedennallo-output)
-  - [Table of contents](#table-of-contents)
-  - [Pipeline overview](#pipeline-overview)
-    - [Alignment](#alignment)
-    - [Assembly](#assembly)
-    - [Assembly variant calling](#assembly-variant-calling)
-    - [CNV calling](#cnv-calling)
-    - [Methylation](#methylation)
-    - [MultiQC](#multiqc)
-    - [Paraphase](#paraphase)
-    - [Phasing](#phasing)
-    - [Pipeline information](#pipeline-information)
-    - [Aligned read QC](#aligned-read-qc)
-      - [Mosdepth](#mosdepth)
-      - [Cramino](#cramino)
-      - [Somalier](#somalier)
-    - [Raw read QC](#raw-read-qc)
-      - [FastQC](#fastqc)
-    - [Repeat calling](#repeat-calling)
-    - [Repeat annotation](#repeat-annotation)
-    - [SNV Annotation](#snv-annotation)
-    - [Ranked Variants](#ranked-variants)
-    - [SV Calling](#sv-calling)
+## Introduction
 
-## Pipeline overview
+This document describes the pipeline output files and the tools used to generate them.
 
-The directories listed below will be created in the results directory after the pipeline has finished:
+## Aligned reads
 
-- `aligned_reads`
-- `assembly_haplotypes`
-- `assembly_variant_calling`
-- `cnv_calling`
-- `methylation`
-- `multiqc`
-- `paraphase`
-- `phasing`
-- `pipeline_info`
-- `qc_aligned_reads`
-- `qc_raw_reads`
-- `repeat_calling`
-- `snv_annotation`
-- `snv_calling`
-- `sv_calling`
+[Minimap2](https://github.com/lh3/minimap2) is used to map the reads to a reference genome. The aligned reads are sorted, merged and indexed using [samtools](https://github.com/samtools/samtools). If the pipeline is run with phasing, the aligned reads will be happlotagged using the active phasing tool.
 
-### Alignment
+| Path                                    | Description                         | Alignment          | Alignment & phasing |
+| --------------------------------------- | ----------------------------------- | ------------------ | ------------------- |
+| `aligned_reads/minimap2/{sample}/*.bam` | Alignment file in bam format        | :white_check_mark: |                     |
+| `aligned_reads/minimap2/{sample}/*.bai` | Index of the corresponding bam file | :white_check_mark: |                     |
 
-[minimap2](https://github.com/lh3/minimap2) is used to map the reads to a reference genome. The aligned reads are sorted, (merged) and indexed using [samtools](https://github.com/samtools/samtools).
+| Path                                                  | Description             | Alignment | Alignment & phasing |
+| ----------------------------------------------------- | ----------------------- | --------- | ------------------- |
+| `aligned_reads/{sample}/{sample}_haplotagged.bam`     | BAM file with haplotags |           | :white_check_mark:  |
+| `aligned_reads/{sample}/{sample}_haplotagged.bam.bai` | Index of the BAM file   |           | :white_check_mark:  |
 
-<details markdown="1">
-<summary>Output files from Alignment</summary>
+## Assembly
 
-- `{outputdir}/aligned_reads/minimap2/{sample}/`
-  - `*.bam`: Alignment file in bam format
-  - `*.bai`: Index of the corresponding bam file
-  </details>
+[Hifiasm](https://github.com/chhylp123/hifiasm) is used to assemble genomes. The assembled haplotypes are then converted to fasta files using [gfastats](https://github.com/vgl-hub/gfastats). A deconstructed version of [dipcall](https://github.com/lh3/dipcall) is used to map the assembled haplotypes back to the reference genome.
 
-### Assembly
+| Path                                                         | Description                                          |
+| ------------------------------------------------------------ | ---------------------------------------------------- |
+| `assembly_haplotypes/gfastats/{sample}/*hap1.p_ctg.fasta.gz` | Assembled haplotype 1                                |
+| `assembly_haplotypes/gfastats/{sample}/*hap2.p_ctg.fasta.gz` | Assembled haplotype 2                                |
+| `assembly_haplotypes/gfastats/{sample}/*.assembly_summary`   | Summary statistics                                   |
+| `assembly_variant_calling/dipcall/{sample}/*hap1.bam`        | Assembled haplotype 1 mapped to the reference genome |
+| `assembly_variant_calling/dipcall/{sample}/*hap1.bai`        | Index of the corresponding BAM file for haplotype 1  |
+| `assembly_variant_calling/dipcall/{sample}/*hap2.bam`        | Assembled haplotype 2 mapped to the reference genome |
+| `assembly_variant_calling/dipcall/{sample}/*hap2.bai`        | Index of the corresponding BAM file for haplotype 2  |
 
-[hifiasm](https://github.com/chhylp123/hifiasm) is used to assemble genomes. The assembled haplotypes are then comverted to fasta files using [gfastats](https://github.com/vgl-hub/gfastats).
+## Methylation pileups
 
-<details markdown="1">
-<summary>Output files from Assembly</summary>
+[Modkit](https://github.com/nanoporetech/modkit) is used to create methylation pileups, producing bedMethyl files for both haplotagged and ungrouped reads. Additionally, methylation information can be viewed in the BAM files, for example in IGV. When phasing is on, modkit outputs pileups per haplotype.
 
-- `{outputdir}/assembly_haplotypes/gfastats/{sample}/`
-  - `*hap1.p_ctg.fasta.gz`: Assembled haplotype 1
-  - `*hap2.p_ctg.fasta.gz`: Assembled haplotype 2
-  - `*.assembly_summary`: Summary statistics
-  </details>
+| Path                                                                         | Description                                               | Alignment          | Alignment & phasing |
+| ---------------------------------------------------------------------------- | --------------------------------------------------------- | ------------------ | ------------------- |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup_phased_*.bed.gz`         | bedMethyl file with summary counts from haplotagged reads |                    | :white_check_mark:  |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup_phased_ungrouped.bed.gz` | bedMethyl file for ungrouped reads                        |                    | :white_check_mark:  |
+| `methylation/modkit/pileup/{sample}/*.modkit_pileup.bed.gz`                  | bedMethyl file with summary counts from all reads         | :white_check_mark: |                     |
+| `methylation/modkit/pileup/{sample}/*.bed.gz.tbi`                            | Index of the corresponding bedMethyl file                 | :white_check_mark: |                     |
 
-### Assembly variant calling
+## MultiQC
 
-A deconstructed version of [dipcall](https://github.com/lh3/dipcall) is used to call variants from the assembled haplotypes. They are also mapped back to the reference genome.
+[MultiQC](http://multiqc.info) generates an HTML report summarizing all samples' QC results and pipeline statistics.
 
-<details markdown="1">
-<summary>Output files from Assembly variant calling</summary>
+| Path                          | Description                               |
+| ----------------------------- | ----------------------------------------- |
+| `multiqc/multiqc_report.html` | HTML report summarizing QC results        |
+| `multiqc/multiqc_data/`       | Directory containing parsed statistics    |
+| `multiqc/multiqc_plots/`      | Directory containing static report images |
 
-> Dipcall produces several files, a full expanation is available [here](https://github.com/lh3/dipcall).
+## Pipeline Information
 
-- `{outputdir}/assembly_variant_calling/dipcall/{sample}/`
+[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) generates reports for troubleshooting, performance, and traceability.
 
-  - `*hap1.bam`: Assembled haplotype 1 mapped to the reference genome
-  - `*hap1.bai`: Index of the corresponding bam file.
-  - `*hap2.bam`: Assembled haplotype 2 mapped to the reference genome
-  - `*hap2.bai`: Index of the corresponding bam file.
+| Path                                    | Description                       |
+| --------------------------------------- | --------------------------------- |
+| `pipeline_info/execution_report.html`   | Execution report                  |
+| `pipeline_info/execution_timeline.html` | Timeline report                   |
+| `pipeline_info/execution_trace.txt`     | Execution trace                   |
+| `pipeline_info/pipeline_dag.dot`        | Pipeline DAG in DOT format        |
+| `pipeline_info/pipeline_report.html`    | Pipeline report                   |
+| `pipeline_info/software_versions.yml`   | Software versions used in the run |
 
-  </details>
+## Phasing
 
-### CNV calling
+[LongPhase](https://github.com/twolinin/longphase), [WhatsHap](https://whatshap.readthedocs.io/en/latest/), or [HiPhase](https://github.com/PacificBiosciences/HiPhase) are used for phasing.
 
-[HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV) is used to call CNVs. It also produces copynumber, depth and MAF tracks loadable in IGV.
+| Path                                                  | Description                   |
+| ----------------------------------------------------- | ----------------------------- |
+| `aligned_reads/{sample}/{sample}_haplotagged.bam`     | BAM file with haplotags       |
+| `aligned_reads/{sample}/{sample}_haplotagged.bam.bai` | Index of the BAM file         |
+| `phased_variants/{sample}/*.vcf.gz`                   | VCF file with phased variants |
+| `phased_variants/{sample}/*.vcf.gz.tbi`               | Index of the VCF file         |
+| `qc/phasing_stats/{sample}/*.blocks.tsv`              | Phase block file              |
+| `qc/phasing_stats/{sample}/*.stats.tsv`               | Phasing statistics file       |
 
-<details markdown="1">
-<summary>Output files from CNV calling</summary>
+## QC
 
-- `{outputdir}/cnv_calling/hificnv/{sample}/`
-  - `*.copynum.bedgraph`: Copy number in bedgraph format
-  - `*.depth.bw`: Depth track in BigWig format
-  - `*.maf.bw`: Minor allele frequencies in BigWig format
-  - `*.vcf.gz`: VCF file containing CNV variants
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-  </details>
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino), [mosdepth](https://github.com/brentp/mosdepth), and [somalier](https://github.com/brentp/somalier) are used for read quality control.
 
-### Methylation
+### FastQC
 
-[modkit](https://github.com/nanoporetech/modkit) is used to create methylation pileups. bedMethyl files are stored both one file with summary counts from reads per haplotag (e.g. HP1, HP2 and ungrouped) and one file with summary counts from all reads. The methylation is also stored in the BAM files and can be viewed directly in IGV.
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) provides general quality metrics for sequenced reads, including information on quality score distribution, per-base sequence content (%A/T/G/C), adapter contamination, and overrepresented sequences. For more details, refer to the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-<details markdown="1">
-<summary>Output files from Methylation</summary>
+| Path                               | Description                                                     |
+| ---------------------------------- | --------------------------------------------------------------- |
+| `qc/fastqc/{sample}/*_fastqc.html` | FastQC report containing quality metrics                        |
+| `qc/fastqc/{sample}/*_fastqc.zip`  | Zip archive with the FastQC report, data files, and plot images |
 
-- `{outputdir}/methylation/modkit/pileup/phased/{sample}/`
+### Mosdepth
 
-  - `*.modkit_pileup_phased_*.bed.gz`: bedMethyl file containing summary counts from reads with haplotags, e.g. 1 or 2
-  - `*.modkit_pileup_phased_ungrouped.bed.gz`: bedMethyl file containing summary counts for ungrouped reads
-  - `*.bed.gz.tbi`: Index of the corresponding bedMethyl file
+[Mosdepth](https://github.com/brentp/mosdepth) is used to report quality control metrics such as coverage and GC content from alignment files.
 
-- `{outputdir}/methylation/modkit/pileup/unphased/{sample}/`
-  - `*.modkit_pileup.bed.gz`: bedMethyl file containing summary counts from all reads
-  - `*.bed.gz.tbi`: Index of the corresponding bedMethyl file
-  </details>
+| Path                                              | Description                                                                                                           | With `--target_regions` | Without `--target_regions` |
+| ------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------- | ----------------------- | -------------------------- |
+| `qc/mosdepth/{sample}/*.mosdepth.global.dist.txt` | Cumulative distribution of bases covered for at least a given coverage value, across chromosomes and the whole genome | :white_check_mark:      | :white_check_mark:         |
+| `qc/mosdepth/{sample}/*.mosdepth.summary.txt`     | Mosdepth summary file                                                                                                 | :white_check_mark:      | :white_check_mark:         |
+| `qc/mosdepth/{sample}/*.mosdepth.region.dist.txt` | Cumulative distribution of bases covered for at least a given coverage value, across regions                          | :white_check_mark:      |                            |
+| `qc/mosdepth/{sample}/*.regions.bed.gz`           | Depth per region                                                                                                      | :white_check_mark:      |
+| `qc/mosdepth/{sample}/*.regions.bed.gz.csi`       | Index of the regions.bed.gz file                                                                                      | :white_check_mark:      |
 
-### MultiQC
+### Cramino
 
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
+[cramino](https://github.com/wdecoster/cramino) is used to analyze both phased and unphased reads.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+| Path                                   | Description                                                                                          |
+| -------------------------------------- | ---------------------------------------------------------------------------------------------------- |
+| `qc/cramino/phased/{sample}/*.arrow`   | Read length and quality in [Apache Arrow](https://arrow.apache.org/docs/format/Columnar.html) format |
+| `qc/cramino/phased/{sample}/*.txt`     | Summary information in text format                                                                   |
+| `qc/cramino/unphased/{sample}/*.arrow` | Read length and quality in [Apache Arrow](https://arrow.apache.org/docs/format/Columnar.html) format |
+| `qc/cramino/unphased/{sample}/*.txt`   | Summary information in text format                                                                   |
 
-<details markdown="1">
-<summary>Output files</summary>
+### Somalier
 
-- `{outputdir}/multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
-  </details>
+[somalier](https://github.com/brentp/somalier) checks relatedness and sex.
 
-### Paraphase
+| Path                                                 | Description                                            |
+| ---------------------------------------------------- | ------------------------------------------------------ |
+| `pedigree/family/{family).ped`                       | PED file updated with somalier-inferred sex per family |
+| `qc/somalier/relate/{project}/{project}.html`        | HTML report                                            |
+| `qc/somalier/relate/{project}/{project}.pairs.tsv`   | Information about sample pairs                         |
+| `qc/somalier/relate/{project}/{project}.samples.tsv` | Information about individual samples                   |
 
-[Paraphase](https://github.com/PacificBiosciences/paraphase) is used to call paralogous genes. For interpreting the output, see <https://github.com/PacificBiosciences/paraphase>.
+### DeepVariant
 
-<details markdown="1">
-<summary>Output files from Paraphase</summary>
+`vcf_stats_report.py` from [DeepVariant](https://github.com/google/deepvariant) is used to generate a html report per sample.
 
-- `{outputdir}/paraphase/{sample}/`
-  - `*.bam`: BAM file with haplotypes grouped by HP and colored by YC
-  - `*.bai`: Index of the corresponding bam file.
-  - `*.json`: Output file summarizing haplotypes and variant calls
-  - `{sample}_paraphase_vcfs/`:
-    - `{sample}_{gene}_vcf`: VCF file per gene
-    - `{sample}_{gene}_vcf.tbi`: Index of the corresponding VCF file
-    </details>
+| Path                                                                  | Description                                 |
+| --------------------------------------------------------------------- | ------------------------------------------- |
+| `qc/deepvariant_vcfstatsreport/{sample}/${sample}.visual_report.html` | Visual report of SNV calls from DeepVariant |
 
-### Phasing
+## Variants
 
-[WhatsHap](https://whatshap.readthedocs.io/en/latest/) or [HiPhase](https://github.com/PacificBiosciences/HiPhase) are used to phase variants and haplotag reads.
+In general, annotated variant calls are output per family while unannotated calls are output per sample.
 
-<details markdown="1">
-<summary>Output files from WhatsHap</summary>
+### Paralogous genes
 
-- `{outputdir}/aligned_reads/{sample}/`
-  - `{sample}_phased.bam`: BAM file with haplotags
-  - `{sample}_phased.bam.bai`: Index of the corresponding bam file
-- `{outputdir}/phasing/whatshap/phase/{sample}/`
-  - `*.vcf.gz`: VCF file with phased variants
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/phasing/whatshap/stats/{sample}/`
-  - `*.blocks.tsv`: File with phase blocks
-  - `*.stats.tsv`: File with phasing statistics
-  </details>
+[Paraphase](https://github.com/PacificBiosciences/paraphase) is used to call paralogous genes.
 
-<details markdown="1">
-<summary>Output files from HiPhase</summary>
+| Path                                                                    | Description                               |
+| ----------------------------------------------------------------------- | ----------------------------------------- |
+| `paraphase/{sample}/*.bam`                                              | BAM file with reads from analysed regions |
+| `paraphase/{sample}/*.bai`                                              | Index of the BAM file                     |
+| `paraphase/{sample}/*.json`                                             | Summary of haplotypes and variant calls   |
+| `paraphase/{sample}/{sample}_paraphase_vcfs/{sample}_{gene}_vcf.gz`     | VCF file per gene                         |
+| `paraphase/{sample}/{sample}_paraphase_vcfs/{sample}_{gene}_vcf.gz.tbi` | Index of the VCF file                     |
 
-- `{outputdir}/aligned_reads/{sample}/`
+### Repeats
 
-  - `{sample}_phased.bam`: BAM file with haplotags
-  - `{sample}_phased.bam.bai`: Index of the corresponding bam file
-
-- `{outputdir}/phasing/hiphase/{snv,sv}/{sample}/`
-
-  - `*.blocks.tsv`: File with phase blocks
-  - `*.stats.tsv.gz`: File with phasing statistics
-  - `*.vcf.gz`: VCF file with phased variants
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-  - `*.summary.tsv`: HiPhase summary file
-
-  </details>
-
-### Pipeline information
-
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `pipeline_info/`
-  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
-  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
-  - Parameters used by the pipeline run: `params.json`.
-
-</details>
-
-### Aligned read QC
-
-[cramino](https://github.com/wdecoster/cramino), [mosdepth](https://github.com/brentp/mosdepth) and [somalier](https://github.com/brentp/somalier) are used for aligned read QC.
-
-##### Mosdepth
-
-[Mosdepth](https://github.com/brentp/mosdepth) is used to report quality control metrics such as coverage, and GC content from alignment files.
-
-<details markdown="1">
-<summary>Output files from Mosdepth</summary>
-
-- `{outputdir}/qc_aligned_reads/mosdepth/{sample}`
-  - `*.mosdepth.global.dist.txt`: This file contains a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value across each chromosome and the whole genome
-  - `*.mosdepth.region.dist.txt`: This file contains a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value across each region, is output if running the pipeline with a BED-file
-  - `*.mosdepth.summary.txt`: Mosdepth ummary file
-  - `*.regions.bed.gz`: Depth per region, is output if running the pipeline with a BED-file
-  - `*.regions.bed.gz.csi`: Index of regions.bed.gz
-  </details>
-
-##### Cramino
+[TRGT](https://github.com/PacificBiosciences/trgt) is used to call repeats.
 
-[cramino](https://github.com/wdecoster/cramino) is run on both phased and unphased reads.
+| Path                                                            | Description                               | Call repeats       | Call & annotate repeats |
+| --------------------------------------------------------------- | ----------------------------------------- | ------------------ | ----------------------- |
+| `repeats/family/{family}/{family}_repeat_expansions.vcf.gz`     | Merged VCF file per family                | :white_check_mark: |                         |
+| `repeats/family/{family}/{family}_repeat_expansions.vcf.gz.tbi` | Index of the VCF file                     | :white_check_mark: |                         |
+| `repeats/sample/{sample}/{sample}_sorted.vcf.gz`                | VCF file with called repeats for a sample | :white_check_mark: | :white_check_mark:      |
+| `repeats/sample/{sample}/{sample}_sorted.vcf.gz.tbi`            | Index of the VCF file                     | :white_check_mark: | :white_check_mark:      |
+| `repeats/sample/{sample}/{sample}_spanning_sorted.bam`          | BAM file with sorted spanning reads       | :white_check_mark: | :white_check_mark:      |
+| `repeats/sample/{sample}/{sample}_spanning_sorted.bai`          | Index of the BAM file                     | :white_check_mark: | :white_check_mark:      |
 
-<details markdown="1">
-<summary>Output files from Cramino</summary>
+[Stranger](https://github.com/Clinical-Genomics/stranger) is used to annotate repeats.
 
-- `{outputdir}/qc_aligned_reads/cramino/phased/{sample}`
-  - `*.arrow`: Read length and quality in [Apache Arrow](https://arrow.apache.org/docs/format/Columnar.html) format
-  - `*.txt`: Summary information in text format
-- `{outputdir}/qc_aligned_reads/cramino/unphased/{sample}`
-  - `*.arrow`: Read length and quality in [Apache Arrow](https://arrow.apache.org/docs/format/Columnar.html) format
-  - `*.txt`: Summary information in text format
-  </details>
+| Path                                                                                | Description                           | Call repeats | Call & annotate repeats |
+| ----------------------------------------------------------------------------------- | ------------------------------------- | ------------ | ----------------------- |
+| `repeat_expansions/family/{family}/{family}_repeat_expansions_annotated.vcf.gz`     | Merged, annotated VCF file per family |              | :white_check_mark:      |
+| `repeat_expansions/family/{family}/{family}_repeat_expansions_annotated.vcf.gz.tbi` | Index of the VCF file                 |              | :white_check_mark:      |
 
-##### Somalier
+### SNVs
 
-[somalier](https://github.com/brentp/somalier) is used to check relatedness and sex.
+[DeepVariant](https://github.com/google/deepvariant) is used to call variants, while [bcftools](https://samtools.github.io/bcftools/bcftools.html) and [GLnexus](https://github.com/dnanexus-rnd/GLnexus) are used for merging variants.
 
-<details markdown="1">
-<summary>Output files from Somalier</summary>
+| Path                                                                  | Description                                                                 | Call SNVs          | Call & annotate SNVs | Call, annotate and rank SNVs |
+| --------------------------------------------------------------------- | --------------------------------------------------------------------------- | ------------------ | -------------------- | ---------------------------- |
+| `snvs/sample/{sample}/{sample}_snv.vcf.gz`                            | VCF file containing called variants with alternative genotypes for a sample | :white_check_mark: | :white_check_mark:   | :white_check_mark:           |
+| `snvs/sample/{sample}/{sample}_snv.vcf.gz.tbi`                        | Index of the corresponding VCF file                                         | :white_check_mark: | :white_check_mark:   | :white_check_mark:           |
+| `snvs/stats/sample/*.stats.txt`                                       | Variant statistics                                                          | :white_check_mark: | :white_check_mark:   | :white_check_mark:           |
+| `qc/deepvariant_vcfstatsreport/{sample}/${sample}.visual_report.html` | Visual report of SNV calls from DeepVariant                                 | :white_check_mark: | :white_check_mark:   | :white_check_mark:           |
+| `snvs/family/{family}/{family}_snv.vcf.gz`                            | VCF file containing called variants for all samples                         | :white_check_mark: |                      |                              |
+| `snvs/family/{family}/{family}_snv.vcf.gz.tbi`                        | Index of the corresponding VCF file                                         | :white_check_mark: |                      |                              |
 
-- `{outputdir}/qc_aligned_reads/somalier/relate/{project}/`
-  - `{project}.html`: HTML report
-  - `{project}.pairs.tsv`: Output information in sample pairs
-  - `{project}.samples.tsv`: Output information per sample
-  </details>
+#### Annotation
 
-### Raw read QC
+[Echtvar](https://github.com/brentp/echtvar) and [VEP](https://www.ensembl.org/vep) are used for annotating SNVs, while [CADD](https://cadd.gs.washington.edu/) is used to annotate INDELs with CADD scores.
 
-[cramino](https://github.com/wdecoster/cramino), [mosdepth](https://github.com/brentp/mosdepth) and [somalier](https://github.com/brentp/somalier) are used for aligned read QC.
+| Path                                                      | Description                                                                    | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
+| --------------------------------------------------------- | ------------------------------------------------------------------------------ | --------- | -------------------- | ---------------------------- |
+| `snvs/sample/{sample}/{sample}_snvs_annotated.vcf.gz`     | VCF file containing annotated variants with alternative genotypes for a sample |           | :white_check_mark:   |                              |
+| `snvs/sample/{sample}/{sample}_snvs_annotated.vcf.gz.tbi` | Index of the annotated VCF file                                                |           | :white_check_mark:   |                              |
+| `snvs/family/{family}/{family}_snvs_annotated.vcf.gz`     | VCF file containing annotated variants per family                              |           | :white_check_mark:   |                              |
+| `snvs/family/{family}/{family}_snvs_annotated.vcf.gz.tbi` | Index of the annotated VCF file                                                |           | :white_check_mark:   |                              |
 
-##### FastQC
+#### Ranking
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+[GENMOD](https://github.com/Clinical-Genomics/genmod) is used to rank the annotated SNVs and INDELs.
 
-<details markdown="1">
-<summary>Output files</summary>
+| Path                                                             | Description                                              | Call SNVs | Call & annotate SNVs | Call, annotate and rank SNVs |
+| ---------------------------------------------------------------- | -------------------------------------------------------- | --------- | -------------------- | ---------------------------- |
+| `snvs/sample/{sample}/{sample}_snvs_annotated_ranked.vcf.gz`     | VCF file with annotated and ranked variants for a sample |           | :white_check_mark:   |
+| `snvs/sample/{sample}/{sample}_snvs_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file                             |           | :white_check_mark:   |
+| `snvs/family/{family}/{family}_snvs_annotated_ranked.vcf.gz`     | VCF file with annotated and ranked variants per family   |           |                      | :white_check_mark:           |
+| `snvs/family/{family}/{family}_snvs_annotated_ranked.vcf.gz.tbi` | Index of the ranked VCF file                             |           |                      | :white_check_mark:           |
 
-- `{outputdir}/qc_raw_reads/fastqc/{sample}/`
-  - `*_fastqc.html`: FastQC report containing quality metrics.
-  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-  </details>
+#### Filtering
 
-### Repeat calling
+[Filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html) can be used to filter variants. These will be output if either of `--filter_variants_hgnc_id` and `--filter_snvs_expression` has been used, and only family VCFs are filtered.
 
-[TRGT](https://github.com/PacificBiosciences/trgt) is used to call repeats.
+| Path                                           | Description                                  |
+| ---------------------------------------------- | -------------------------------------------- |
+| `snvs/{family}/{family}_*_filtered.vcf.gz`     | VCF file with filtered variants for a family |
+| `snvs/{family}/{family}_*_filtered.vcf.gz.tbi` | Index of the filtered VCF file               |
 
-<details markdown="1">
-<summary>Output files from TRGT</summary>
+!!!tip
 
-- `{outputdir}/repeat_calling/trgt/multi_sample/{project}/`
-  - `*.vcf.gz`: Merged VCF for all samples
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/repeat_calling/trgt/single_sample/{sample}/`
-  - `*.vcf.gz`: VCF with called repeats
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-  - `*.bam`: BAM file with sorted spanning reads
-  - `*.bai`: Index of the corresponding bam file
-  </details>
+    Filtered variants are output alongside unfiltered variants as additional files.
 
-### Repeat annotation
+### SVs (and CNVs)
 
-[Stranger](https://github.com/Clinical-Genomics/stranger) is used to annotate repeats.
+[Severus](https://github.com/KolmogorovLab/Severus) or [Sniffles](https://github.com/fritzsedlazeck/Sniffles) are used to call structural variants, while [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV) is used to call CNVs. HiFiCNV also produces copy number, depth, and MAF [visualization tracks](#visualization-tracks).
 
-<details markdown="1">
-<summary>Output files from Stranger</summary>
+!!!info "Variant merging strategies"
 
-- `{outputdir}/repeat_annotation/stranger/{sample}`
-  - `*.vcf.gz`: Annotated VCF
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-  </details>
+    SV and CNV calls are output unmerged per sample, while the family files are first merged between samples for SVs and CNVs separately, then the merged SV and CNV files are merged again, with priority given to coordinates from the SV calls.
 
-### SNV Annotation
+| Path                                                            | Description                                  | Call SVs           | Call CNVs          | Call SVs & CNVs    |
+| --------------------------------------------------------------- | -------------------------------------------- | ------------------ | ------------------ | ------------------ |
+| `svs/sample/{sample}/{sample}_svs.vcf.gz`                       | VCF file with SVs per sample                 | :white_check_mark: |                    | :white_check_mark: |
+| `svs/sample/{sample}/{sample}_svs.vcf.gz.tbi`                   | VCF file with SVs per sample                 | :white_check_mark: |                    | :white_check_mark: |
+| `svs/sample/{sample}/{sample}_cnvs.vcf.gz`                      | VCF file with CNVs per sample                |                    | :white_check_mark: | :white_check_mark: |
+| `svs/sample/{sample}/{sample}_cnvs.vcf.gz.tbi`                  | VCF file with CNVs per sample                |                    | :white_check_mark: | :white_check_mark: |
+| `svs/family/{family_id}/{family_id}_svs_merged.vcf.gz`          | VCF file with merged SVs per family          | :white_check_mark: |                    |                    |
+| `svs/family/{family_id}/{family_id}_svs_merged.vcf.gz.tbi`      | Index of the merged VCF file                 | :white_check_mark: |                    |                    |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged.vcf.gz`     | VCF file with merged CNVs and SVs per family |                    |                    | :white_check_mark: |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged.vcf.gz.tbi` | Index of the merged VCF file                 |                    |                    | :white_check_mark: |
 
-[echtvar](https://github.com/brentp/echtvar) and [VEP](https://www.ensembl.org/vep) are used to annotate small variants.
-[bcftools](https://samtools.github.io/bcftools/) is used to generate statistics.
+#### Annotation
 
-<details markdown="1">
-<summary>Output files from SNV Annotation</summary>
+[SVDB](https://github.com/J35P312/SVDB) and [VEP](https://www.ensembl.org/vep) are used to annotate structural variants.
 
-- `{outputdir}/databases/echtvar/encode/{project}/`
-  - `*.zip`: Database with AF and AC for all samples run
-- `{outputdir}/snvs/{single_sample/{sample}/`
-  - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants with alternative genotypes from a certain sample
-  - `*_snvs_annotated*.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/snvs/multi_sample/{project}/`
-  - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants from all samples
-  - `*_snvs_annotated*.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/snvs/stats/single_sample/`
-  - `*.stats.txt`: Variant statistics
-  </details>
+| Path                                                                      | Description                                                | Call & annotate SVs |  Call & annotate SVs & CNVs |
+| ------------------------------------------------------------------------- | ---------------------------------------------------------- | ------------------- | --------------------------- |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged_annotated.vcf.gz`     | VCF file with merged and annotated CNVs and SVs per family |                     | :white_check_mark:          |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged_annotated.vcf.gz.tbi` | Index of the merged VCF file                               |                     | :white_check_mark:          |
+| `svs/family/{family_id}/{family_id}_svs_merged_annotated.vcf.gz`          | VCF file with merged and annotated SVs per family          | :white_check_mark:  |
+| `svs/family/{family_id}/{family_id}_svs_merged_annotated.vcf.gz.tbi`      | Index of the merged VCF file                               | :white_check_mark:  |
 
-### Ranked variants
+#### Ranking
 
-#### Filter_vep
+[GENMOD](https://github.com/Clinical-Genomics/genmod) is used to rank the annotated SVs.
 
-[filter_vep from VEP](https://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html) is used to subset the variants based on a list of HGNC ID:s. Typical use case is that you want to filter your results to only include variants in a predefined set of clinically relevant genes. This step is optional and can be disabled by using the flag `--skip_vep_filter`. You will always get the complete VCF together with the clinical VCF.
+| Path                                                                             | Description                                                        | Rank SVs           | Rank SVs & CNVs    |
+| -------------------------------------------------------------------------------- | ------------------------------------------------------------------ | ------------------ | ------------------ |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged_annotated_ranked.vcf.gz`     | VCF file with merged, annotated and ranked CNVs and SVs per family |                    | :white_check_mark: |
+| `svs/family/{family_id}/{family_id}_cnvs_svs_merged_annotated_ranked.vcf.gz.tbi` | Index of the merged VCF file                                       |                    | :white_check_mark: |
+| `svs/family/{family_id}/{family_id}_svs_merged_annotated_ranked.vcf.gz`          | VCF file with merged, annotated and ranked SVs per family          | :white_check_mark: |                    |
+| `svs/family/{family_id}/{family_id}_svs_merged_annotated_ranked.vcf.gz.tbi`      | Index of the merged VCF file                                       | :white_check_mark: |                    |
 
-#### GENMOD
+#### Filtering
 
-[GENMOD](https://github.com/Clinical-Genomics/genmod) is a simple to use command line tool for annotating and analyzing genomic variations in the VCF file format. GENMOD can annotate genetic patterns of inheritance in vcf files with single or multiple families of arbitrary size. Each variant will be assigned a predicted pathogenicity score. The score will be given both as a raw score and a normalized score with values between 0 and 1. The tags in the INFO field are `RankScore` and `RankScoreNormalized`. The score can be configured to fit your annotations and preferences by modifying the score config file.
+[Filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html) can be used to filter variants. These will be output if either of `--filter_variants_hgnc_id` and `--filter_svs_expression` has been used, and only family VCFs are filtered.
 
-<details markdown="1">
-<summary>Output files</summary>
+| Path                                          | Description                                  |
+| --------------------------------------------- | -------------------------------------------- |
+| `svs/{family}/{family}_*_filtered.vcf.gz`     | VCF file with filtered variants for a family |
+| `svs/{family}/{family}_*_filtered.vcf.gz.tbi` | Index of the filtered VCF file               |
 
-- `{outputdir}/snvs/single_sample/{sample}/`
-  - `{sample}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants with alternative genotypes from a certain sample
-  - `{sample}_snv_annotated_ranked.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/snvs/multi_sample/{project}/`
-  - `{project}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants from all samples
-  - `{project}_snv_annotated_ranked.vcf.gz.tbi`: Index of the corresponding VCF file
-  </details>
+!!!tip
 
-### SV Calling
+    Filtered variants are output alongside unfiltered variants as additional files.
 
-[Sniffles](https://github.com/fritzsedlazeck/Sniffles) is used to call and merge structural variants.
+## Visualization Tracks
 
-<details markdown="1">
-<summary>Output files from SNV Calling</summary>
+[HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV) is used to call CNVs, but it also produces copy number, depth, and MAF tracks that can be visualized in for example IGV.
 
-- `{outputdir}/sv_calling/multi_sample/{project}`
-  - `*.vcf.gz`: VCF with variants
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-- `{outputdir}/sv_calling/single_sample/{sample}`
-  - `*.snf`: Sniffles SNF file
-  - `*.vcf.gz`: VCF with variants
-  - `*.vcf.gz.tbi`: Index of the corresponding VCF file
-  </details>
+| Path                                               | Description                               |
+| -------------------------------------------------- | ----------------------------------------- |
+| `visualization_tracks/{sample}/*.copynum.bedgraph` | Copy number in bedgraph format            |
+| `visualization_tracks/{sample}/*.depth.bw`         | Depth track in BigWig format              |
+| `visualization_tracks/{sample}/*.maf.bw`           | Minor allele frequencies in BigWig format |
diff --git a/docs/parameters.md b/docs/parameters.md
index 890af543..0acde4c8 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -1,177 +1,118 @@
+# genomic-medicine-sweden/nallo pipeline parameters
 
+Long-read variant calling pipeline
 
-# genomic-medicine-sweden/nallo pipeline parameters                                                                                                 
-                                                                                                                                                    
-Long-read variant calling pipeline                                                                                                                  
-                                                                                                                                                    
-## Workflow skip options                                                                                                                            
-                                                                                                                                                    
-Allows skipping certain parts of the pipeline                                                                                                       
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `skip_aligned_read_qc` | Skip QC of aligned reads | `boolean` | False |  |  |                                                                     
-| `skip_raw_read_qc` | Skip QC of unaligned (raw) reads | `boolean` | False |  |  |                                                                 
-| `skip_short_variant_calling` | Skip short variant calling | `boolean` | False |  |  |                                                             
-| `skip_assembly_wf` | Skip genome assembly and assembly variant calling | `boolean` | False |  |  |                                                
-| `skip_mapping_wf` | Skip read mapping (alignment) | `boolean` | False |  |  |                                                                     
-| `skip_methylation_wf` | Skip generation of methylation pileups | `boolean` | False |  |  |                                                        
-| `skip_repeat_calling` | Skip tandem repeat calling | `boolean` | False |  |  |                                                                    
-| `skip_repeat_annotation` | Skip tandem repeat annotation | `boolean` | False |  |  |                                                              
-| `skip_phasing_wf` | Skip phasing of variants and haplotagging of reads | `boolean` | False |  |  |                                                
-| `skip_snv_annotation` | Skip short variant annotation | `boolean` | False |  |  |                                                                 
-| `skip_cnv_calling` | Skip CNV calling | `boolean` | False |  |  |                                                                                 
-| `skip_call_paralogs` | Skip the calling of specific paralogous genes | `boolean` | False |  |  |                                                  
-| `skip_rank_variants` | Skip ranking of short variants | `boolean` | False |  |  |                                                                 
-                                                                                                                                                    
-## Input/output options                                                                                                                             
-                                                                                                                                                    
-Define where the pipeline should find input data and save output data.                                                                              
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>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.</small></details>| `string` |  | True |  |                          
-| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` |  
-| True |  |                                                                                                                                         
-| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary 
-e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to   
-specify this on the command line for every run.</small></details>| `string` |  |  |  |                                                              
-| `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` |  |  |  |               
-                                                                                                                                                    
-## Reference genome options                                                                                                                         
-                                                                                                                                                    
-Reference genome related files and options required for the workflow.                                                                               
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `fasta` | Reference genome | `string` |  |  |  |                                                                                                  
-| `genome` | Name of iGenomes reference. <details><summary>Help</summary><small>If using a reference genome configured in the pipeline using        
-iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files    
-e.g. `--genome GRCh38`. <br><br>See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.</small></details>|       
-`string` |  |  |  |                                                                                                                                 
-| `igenomes_ignore` | Do not load the iGenomes reference config. <details><summary>Help</summary><small>Do not load `igenomes.config` when running  
-the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in                                     
-`igenomes.config`.</small></details>| `boolean` | True |  | True |                                                                                  
-                                                                                                                                                    
-## Institutional config options                                                                                                                     
-                                                                                                                                                    
-Parameters used to describe centralised config profiles. These should not be edited.                                                                
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `custom_config_version` | Git commit id for Institutional configs. | `string` | master |  | True |                                                
-| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will  
-not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you 
-should download the files from the repo and tell Nextflow where to find them with this parameter.</small></details>| `string` |                     
-https://raw.githubusercontent.com/nf-core/configs/master |  | True |                                                                                
-| `config_profile_name` | Institutional config name. | `string` |  |  | True |                                                                      
-| `config_profile_description` | Institutional config description. | `string` |  |  | True |                                                        
-| `config_profile_contact` | Institutional config contact information. | `string` |  |  | True |                                                    
-| `config_profile_url` | Institutional config URL link. | `string` |  |  | True |                                                                   
-                                                                                                                                                    
-## Max job request options                                                                                                                          
-                                                                                                                                                    
-Set the top limit for requested resources for any single job.                                                                                       
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for
-the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`</small></details>| `integer` | 16 |  | True |                        
-| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit
-for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 
-128.GB |  | True |                                                                                                                                  
-| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for
-the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`</small></details>| `string` | 240.h |  
-| True |                                                                                                                                            
-                                                                                                                                                    
-## Generic options                                                                                                                                  
-                                                                                                                                                    
-Less common options for the pipeline, typically set in a config file.                                                                               
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `help` | Display help text. | `boolean` |  |  | True |                                                                                            
-| `version` | Display version and exit. | `boolean` |  |  | True |                                                                                  
-| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>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.</small></details>| `string` | copy |  |  
-True |                                                                                                                                              
-| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send 
-a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` |  |  | True |
-| `plaintext_email` | Send plain-text email instead of HTML. | `boolean` |  |  | True |                                                             
-| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB |  | True |                       
-| `monochrome_logs` | Do not use coloured log outputs. | `boolean` |  |  | True |                                                                   
-| `hook_url` | Incoming hook URL for messaging service <details><summary>Help</summary><small>Incoming hook URL for messaging service. Currently, MS
-Teams and Slack are supported.</small></details>| `string` |  |  | True |                                                                           
-| `multiqc_config` | Custom config file to supply to MultiQC. | `string` |  |  | True |                                                             
-| `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` |  |  | True |           
-| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` |  |  |  |                   
-| `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True |  | True |                           
-| `validationShowHiddenParams` | Show all params when using `--help` <details><summary>Help</summary><small>By default, parameters set as _hidden_  
-in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all           
-parameters.</small></details>| `boolean` |  |  | True |                                                                                             
-| `validationSkipDuplicateCheck` | nf-validation related parameter | `boolean` |  |  | True |                                                       
-| `validationS3PathCheck` | Boolean whether to validate validate AWS S3 paths | `boolean` |  |  | True |                                            
-| `monochromeLogs` | Boolean whether to color nf-validation logs | `boolean` |  |  | True |                                                         
-                                                                                                                                                    
-## Workflow options                                                                                                                                 
-                                                                                                                                                    
-Workflow options specific to genomic-medicine-sweden/nallo                                                                                          
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `preset` | Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`) | `string` | revio | 
-True |  |                                                                                                                                           
-| `variant_caller` | Which short variant software to use (`deepvariant`) | `string` | deepvariant |  |  |                                           
-| `phaser` | Which phasing software to use (`whatshap`, `hiphase_snv`, `hiphase_sv`) | `string` | whatshap |  |  |                                  
-| `hifiasm_mode` | Run hifiasm in hifi-only or hifi-trio mode (`hifi-only`, `trio-binning`) | `string` | hifi-only |  |  |                          
-| `parallel_alignments` | If parallel_alignments is bigger than 1, input files will be split and aligned in parallel to reduce processing time. |   
-`integer` | 1 |  |  |                                                                                                                               
-| `parallel_snv` | If parallel_snv is bigger than 1, short variant calling will be done in parallel to reduce processing time. | `integer` | 13 |  |
-|                                                                                                                                                   
-| `vep_cache_version` | VEP cache version | `integer` | 110 |  |  |                                                                                 
-| `vep_plugin_files` | A csv file with paths to vep plugin files. pLI and LoFtool are required. | `string` |  |  |  |                               
-| `deepvariant_model_type` | Sets the model type used for DeepVariant. This is set automatically using `--preset` by default. | `string` | PACBIO | 
-| True |                                                                                                                                            
-                                                                                                                                                    
-## File inputs                                                                                                                                      
-                                                                                                                                                    
-The different files that are required. Some are only required by certain workflows, see the usage documentation.                                    
-                                                                                                                                                    
-| Parameter | Description | Type | Default | Required | Hidden |                                                                                    
-|-----------|-----------|-----------|-----------|-----------|-----------|                                                                           
-| `cadd_prescored` | Path to a directory containing prescored indels for CADD. <details><summary>Help</summary><small>This folder contains the      
-compressed files and indexes that would otherwise be in data/prescored folder as described in                                                       
-https://github.com/kircherlab/CADD-scripts/#manual-installation.</small></details>| `string` |  |  |  |                                             
-| `cadd_resources` | Path to a directory containing CADD annotations. <details><summary>Help</summary><small>This folder contains the uncompressed  
-files that would otherwise be in data/annotation folder as described in                                                                             
-https://github.com/kircherlab/CADD-scripts/#manual-installation.</small></details>| `string` |  |  |  |                                             
-| `par_regions` | Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant | `string` |  |  |  |                                 
-| `tandem_repeats` | A tandem repeat BED file for sniffles | `string` |  |  |  |                                                                    
-| `trgt_repeats` | A BED file with repeats to be genotyped with TRGT | `string` |  |  |  |                                                          
-| `snp_db` | A csv file with echtvar databases to annotate SNVs with | `string` |  |  |  |                                                          
-| `variant_catalog` | A variant catalog json-file for stranger | `string` |  |  |  |                                                                
-| `variant_consequences_snv` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating     
-genomic SNVs. <details><summary>Help</summary><small>For more information check                                                                     
-https://ensembl.org/info/genome/variation/prediction/predicted_data.html</small></details>| `string` |  |  |  |                                     
-| `vep_cache` | A path to the VEP cache location | `string` |  |  |  |                                                                              
-| `bed` | A BED file with regions of interest, used to limit short variant calling. | `string` |  |  |  |                                           
-| `hificnv_xy` | A BED file containing expected copy number regions for XY samples. | `string` |  |  |  |                                           
-| `hificnv_xx` | A BED file containing expected copy number regions for XX samples. | `string` |  |  |  |                                           
-| `hificnv_exclude` | A BED file specifying regions to exclude with HiFiCNV, such as centromeres. | `string` |  |  |  |                             
-| `reduced_penetrance` | A file with gene ids that have reduced penetrance. For use with genmod. | `string` |  |  |  |                              
-| `score_config_snv` | A SNV rank model config file for genmod. | `string` |  |  |  |                                                               
-| `somalier_sites` | A VCF of known polymorphic sites for somalier | `string` |  |  |  |                                                            
-| `validationFailUnrecognisedParams` | Validation of parameters fails when an unrecognised parameter is found.                                      
-<details><summary>Help</summary><small>By default, when an unrecognised parameter is found, it returns a warning.</small></details>| `boolean` |  | 
-| True |                                                                                                                                            
-| `validationLenientMode` | Validation of parameters in lenient more. <details><summary>Help</summary><small>Allows string values that are parseable
-as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode).</small></details>|   
-`boolean` |  |  | True |                                                                                                                            
-| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` |                                   
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ |  | True |                                                                
-                                                                                                                                                    
+## Workflow skip options
 
+Allows skipping certain parts of the pipeline
 
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `skip_qc` | Skip QC of reads | `boolean` | False |  |  |
+| `skip_snv_calling` | Skip short variant calling | `boolean` | False |  |  |
+| `skip_genome_assembly` | Skip genome assembly and assembly variant calling | `boolean` | False |  |  |
+| `skip_alignment` | Skip read mapping (alignment) | `boolean` | False |  |  |
+| `skip_methylation_pileups` | Skip generation of methylation pileups | `boolean` | False |  |  |
+| `skip_repeat_calling` | Skip tandem repeat calling | `boolean` | False |  |  |
+| `skip_repeat_annotation` | Skip tandem repeat annotation | `boolean` | False |  |  |
+| `skip_phasing` | Skip phasing of variants and haplotagging of reads | `boolean` | False |  |  |
+| `skip_snv_annotation` | Skip short variant annotation | `boolean` | False |  |  |
+| `skip_sv_annotation` | Skip structural variant annotation | `boolean` | False |  |  |
+| `skip_cnv_calling` | Skip CNV calling | `boolean` | False |  |  |
+| `skip_call_paralogs` | Skip the calling of specific paralogous genes | `boolean` | False |  |  |
+| `skip_rank_variants` | Skip ranking of short variants | `boolean` | False |  |  |
+
+## Input/output options
+
+Define where the pipeline should find input data and save output data.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>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.</small></details>| `string` |  | True |  |
+| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` |  | True |  |
+| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.</small></details>| `string` |  |  |  |
+| `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` |  |  |  |
+| `cadd_prescored_indels` | Path to a directory containing prescored indels for CADD. <details><summary>Help</summary><small>This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.</small></details>| `string` |  |  |  |
+| `cadd_resources` | Path to a directory containing CADD annotations. <details><summary>Help</summary><small>This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.</small></details>| `string` |  |  |  |
+| `par_regions` | Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant | `string` |  |  |  |
+| `tandem_repeats` | A tandem repeat BED file for sniffles | `string` |  |  |  |
+| `trgt_repeats` | A BED file with repeats to be genotyped with TRGT | `string` |  |  |  |
+| `echtvar_snv_databases` | A csv file with echtvar databases to annotate SNVs with | `string` |  |  |  |
+| `svdb_sv_databases` | Databases used for structural variant annotation in vcf format. <details><summary>Help</summary><small>Path to comma-separated file containing information about the databases used for structural variant annotation.</small></details>| `string` |  |  |  |
+| `stranger_repeat_catalog` | A variant catalog json-file for stranger | `string` |  |  |  |
+| `variant_consequences_snvs` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` |  |  |  |
+| `variant_consequences_svs` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` |  |  |  |
+| `vep_cache` | A path to the VEP cache location | `string` |  |  |  |
+| `target_regions` | A BED file with regions of interest, used to limit variant calling. | `string` |  |  |  |
+| `hificnv_expected_xy_cn` | A BED file containing expected copy number regions for XY samples. | `string` |  |  |  |
+| `hificnv_expected_xx_cn` | A BED file containing expected copy number regions for XX samples. | `string` |  |  |  |
+| `hificnv_excluded_regions` | A BED file specifying regions to exclude with HiFiCNV, such as centromeres. | `string` |  |  |  |
+| `genmod_reduced_penetrance` | A file with gene ids that have reduced penetrance. For use with genmod. | `string` |  |  |  |
+| `genmod_score_config_snvs` | A SNV rank model config file for genmod. | `string` |  |  |  |
+| `genmod_score_config_svs` | A SV rank model config file for genmod. | `string` |  |  |  |
+| `somalier_sites` | A VCF of known polymorphic sites for somalier | `string` |  |  |  |
+| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/ |  | True |
+
+## Reference genome options
+
+Reference genome related files and options required for the workflow.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `fasta` | Reference genome | `string` |  |  |  |
+
+## Institutional config options
+
+Parameters used to describe centralised config profiles. These should not be edited.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `custom_config_version` | Git commit id for Institutional configs. | `string` | master |  | True |
+| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.</small></details>| `string` | https://raw.githubusercontent.com/nf-core/configs/master |  | True |
+| `config_profile_name` | Institutional config name. | `string` |  |  | True |
+| `config_profile_description` | Institutional config description. | `string` |  |  | True |
+| `config_profile_contact` | Institutional config contact information. | `string` |  |  | True |
+| `config_profile_url` | Institutional config URL link. | `string` |  |  | True |
+
+## Generic options
+
+Less common options for the pipeline, typically set in a config file.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `version` | Display version and exit. | `boolean` |  |  | True |
+| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>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.</small></details>| `string` | copy |  | True |
+| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` |  |  | True |
+| `plaintext_email` | Send plain-text email instead of HTML. | `boolean` |  |  | True |
+| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB |  | True |
+| `monochrome_logs` | Do not use coloured log outputs. | `boolean` |  |  | True |
+| `hook_url` | Incoming hook URL for messaging service <details><summary>Help</summary><small>Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.</small></details>| `string` |  |  | True |
+| `multiqc_config` | Custom config file to supply to MultiQC. | `string` |  |  | True |
+| `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` |  |  | True |
+| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` |  |  |  |
+| `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True |  | True |
+
+## Workflow options
+
+Workflow options specific to genomic-medicine-sweden/nallo
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `preset` | Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`) | `string` | revio | True |  |
+| `snv_caller` | Which short variant software to use (`deepvariant`) | `string` | deepvariant |  |  |
+| `sv_caller` | Which structural variant caller to use (`severus`, `sniffles`) | `string` | severus |  |  |
+| `phaser` | Which phasing software to use (`longphase`, `whatshap`, `hiphase`) | `string` | longphase |  |  |
+| `hifiasm_mode` | Run hifiasm in hifi-only or hifi-trio mode (`hifi-only`, `trio-binning`) | `string` | hifi-only |  |  |
+| `alignment_processes` | If alignment_processes is bigger than 1, input files will be split and aligned in parallel to reduce processing time. | `integer` | 8 |  |  |
+| `snv_calling_processes` | If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time. | `integer` | 13 |  |  |
+| `vep_cache_version` | VEP cache version | `integer` | 110 |  |  |
+| `vep_plugin_files` | A csv file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required. | `string` |  |  |  |
+| `filter_variants_hgnc_ids` | A tsv/csv file with a `hgnc_ids` column header, and then one numerical HGNC ID per row. E.g. `4281` or `HGNC:4281`. | `string` |  |  |  |
+| `filter_snvs_expression` | An expression that is passed to bcftools view to filter SNVs, e.g. --filter_snvs_expression "-e 'INFO/AQ>60'" | `string` |  |  |  |
+| `filter_svs_expression` | An expression that is passed to bcftools view to filter SVs, e.g. --filter_svs_expression "-e 'INFO/AQ>60'" | `string` |  |  |  |
+| `deepvariant_model_type` | Sets the model type used for DeepVariant. This is set automatically using `--preset` by default. | `string` | PACBIO |  | True |
+| `minimap2_read_mapping_preset` | Sets the minimap2-preset (-x) for read alignment. This is set automatically using the pipeline `--preset` by default. | `string` | map-hifi |  | True |
+| `extra_modkit_options` | Extra options to modkit, used for test profile. | `string` |  |  | True |
+| `extra_vep_options` | Extra options to VEP, used for test profile. | `string` |  |  | True |
+| `extra_paraphase_options` | Extra options to Paraphase, used for test profile. | `string` |  |  | True |
+| `extra_hifiasm_options` | Extra options to hifiasm, used for test profile. | `string` |  |  | True |
diff --git a/docs/usage.md b/docs/usage.md
index c4ed524c..1f95dcb3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,14 +1,13 @@
 # genomic-medicine-sweden/nallo: Usage
 
-## Introduction
-
-genomic-medicine-sweden/nallo is a bioinformatics analysis pipeline to analyse long-read data.
-
 ## Prerequisites
 
-1. Install Nextflow (>=22.10.1) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation)
+1. Install Nextflow (>=24.04.2) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation)
 2. Install one of the following technologies for full pipeline reproducibility: Docker, Singularity, Podman, Shifter or Charliecloud.
-   > Almost all nf-core pipelines give you the option to use conda as well. However, some tools used in the nallo pipeline do not have a conda package so we do not support conda at the moment.
+
+!!!warning
+
+    Almost all nf-core pipelines give you the option to use conda as well. However, some tools used in genomic-medicine-sweden/nallo do not have a conda package so we do not support conda at the moment.
 
 ## Getting started
 
@@ -22,8 +21,10 @@ nextflow run genomic-medicine-sweden/nallo \
     --outdir <OUTDIR>
 ```
 
-> Check [nf-core/configs](https://github.com/nf-core/configs/tree/master/conf) to see if a custom config file to run nf-core pipelines already exists for your institute. If so, you can simply use `-profile test,<institute>` in your command. This enables the appropriate package manager and sets the appropriate execution settings for your machine.
-> NB: The order of profiles is important! They are loaded in sequence, so later profiles can overwrite earlier profiles.
+!!!note
+
+    Check [nf-core/configs](https://github.com/nf-core/configs/tree/master/conf) to see if a custom config file to run nf-core pipelines already exists for your institute. If so, you can simply use `-profile test,<institute>` in your command. This enables the appropriate package manager and sets the appropriate execution settings for your machine.
+    NB: The order of profiles is important! They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
 Running the command creates the following files in your working directory
 
@@ -34,8 +35,9 @@ work                # Directory containing the Nextflow working files
 # Other Nextflow hidden files, like history of pipeline logs.
 ```
 
-> [!NOTE]
-> The default cpu and memory configurations used in nallo are written keeping the test profile (and dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform.
+!!!note
+
+    The default cpu and memory configurations used in nallo are written keeping the test profile (and dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform.
 
 ### Updating the pipeline
 
@@ -45,9 +47,9 @@ The above command downloads the pipeline from GitHub, caches it, and tests it on
 
 Running the pipeline on real data involves three steps:
 
-1. Preparing a samplesheet with your data
-2. Gather required files and references
-3. Supply samplesheet, refeferences and files and run the pipeline
+1. Prepare a samplesheet with your data
+2. Gather the required files and references
+3. Supply the samplesheet, reference files and run the pipeline
 
 ## Samplesheet
 
@@ -57,7 +59,7 @@ First, you will need to create a samplesheet with information about the samples
 --input '[path to samplesheet file]'
 ```
 
-It has to be a comma-separated file with 7 columns, and a header row as shown in the example below:
+It has to be a comma-separated file with seven columns and a header row, as shown in the example below:
 
 ```console
 project,sample,file,family_id,paternal_id,maternal_id,sex,phenotype
@@ -67,7 +69,7 @@ testrun,HG003,/path/to/HG003.bam,FAM,0,0,2,1
 
 | Fields        | Description                                                                                                                       |
 | ------------- | --------------------------------------------------------------------------------------------------------------------------------- |
-| `project`     | Project name must be provided and cannot contain spaces, needs to be the same for all samples."                                   |
+| `project`     | Project name must be provided and cannot contain spaces, needs to be the same for all samples.                                    |
 | `sample`      | Custom sample name, cannot contain spaces.                                                                                        |
 | `file`        | Absolute path to gzipped FASTQ or BAM file. File has to have the extension ".fastq.gz", .fq.gz" or ".bam".                        |
 | `family_id`   | Family ID must be provided and cannot contain spaces. If no family ID is available use the same ID as sample.                     |
@@ -76,165 +78,176 @@ testrun,HG003,/path/to/HG003.bam,FAM,0,0,2,1
 | `sex`         | Sex must be provided as 0, 1 or 2 (0=unknown; 1=male; 2=female). If sex is unknown it will be assigned automatically if possible. |
 | `phenotype`   | Affected status of patient (0 = missing; 1=unaffected; 2=affected).                                                               |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+## Presets
 
-## Preset
+This pipeline comes with three different presets that should be set with the `--preset` parameter: `revio` (default), `pacbio` or `ONT_R10`. The preset parameter controls certain technology specific tools and parameters.
 
-This pipeline comes with three different presets that should be set with the `--preset` parameter
+!!!info "Preset effects on subworkflows"
 
-- `revio` (default)
-- `pacbio`
-- `ONT_R10`
-
-`--skip_assembly_wf` and `--skip_repeat_wf` will be set to true for `ONT_R10` and `--skip_methylation_wf` will be set to true for `pacbio`, meaning these subworkflows are not run.
+    - `--skip_genome_assembly` and `--skip_repeat_wf` will be set to `true` for `ONT_R10`
+    - `--skip_methylation_pileups` will be set to `true` for `pacbio`
 
 ## Subworkflows
 
-As indicated above, this pipeline is divided into multiple subworkflows, each with its own input requirements and outputs. By default, all subworklows are active, and thus all mandatory input files are required.
+As indicated above, this pipeline is divided into multiple subworkflows, each with their own input requirements and outputs. By default all subworklows are active, and thus all mandatory input files are required.
+
+### Required parameters
 
-The only parameter mandatory for all subworkflows is the `--input` and `--outdir` parameters, all other parameters are determined by the active subworkflows. If you would run `nextflow run genomic-medicine-sweden/nallo -profile docker --outdir results --input samplesheet.csv`
+The only mandatory parameters for all subworkflows are the `--input` and `--outdir` parameters, all other parameters are determined by the active subworkflows.
+
+For example, if you would run `nextflow run genomic-medicine-sweden/nallo -profile docker --outdir results --input samplesheet.csv`, the pipeline will would to guide you through which files are required:
 
 ```
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  --skip_assembly_wf is NOT active, the following files are required: --dipcall_par
-  --skip_snv_annotation is NOT active, the following files are required: --snp_db
-  --skip_mapping_wf is NOT active, the following files are required: --somalier_sites
+  --skip_genome_assembly is NOT active, the following files are required: --par_regions
+  --skip_snv_annotation is NOT active, the following files are required: --echtvar_snv_databases
+  --skip_alignment is NOT active, the following files are required: --somalier_sites
   --skip_snv_annotation is NOT active, the following files are required: --vep_cache
   ...
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ```
 
-The pipeline will try to guide you through which files are required, but a thorough description is provided below.
+A thorough description of the required files are provided below.
+
+### Skipping subworkflows
 
-Additionally, if you want to skip a subworkflow, you will need to explicitly state to skip all subworklow that relies on it. For example, `nextflow run genomic-medicine-sweden/nallo -profile docker --outdir results --input samplesheet.csv --skip_mapping_wf` will tell you
+If you want to skip a subworkflow, you will need to explicitly state to skip all subworkflows that rely on it.
+
+For example, `nextflow run genomic-medicine-sweden/nallo -profile docker --outdir results --input samplesheet.csv --skip_alignment` will tell you
 
 ```
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  --skip_mapping_wf is active, the pipeline has to be run with: --skip_aligned_read_qc --skip_assembly_wf --skip_call_paralogs --skip_short_variant_calling --skip_snv_annotation --skip_cnv_calling --skip_phasing_wf --skip_rank_variants --skip_repeat_calling --skip_repeat_annotation --skip_methylation_wf
+  --skip_alignment is active, the pipeline has to be run with: --skip_qc --skip_genome_assembly --skip_call_paralogs --skip_snv_calling --skip_snv_annotation --skip_cnv_calling --skip_phasing --skip_rank_variants --skip_repeat_calling --skip_repeat_annotation --skip_methylation_pileups
   ...
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ```
 
 Because almost all other subworkflows relies on the mapping subworkflow.
 
-If you want to run the pipeline without any other input files than `--input samplesheet.csv`, all of the above skips will need to be active, and the pipeline will run only unaligned read QC.
-
 ## Reference files and parameters
 
-As descibed above, the files required depend on the active subworkflows. All parameters are listed [here](parameters.md), but the most useful parameters needed to run the pipeline described in more detail below.
+All parameters are listed in the [parameters section](parameters.md), but the most useful parameters needed to run the pipeline described in more detail below.
 
-### Raw read QC (`--skip_raw_read_qc`)
+### Alignment
 
-This subworkflow requires no additional files.
+The majority of subworkflows depend on the alignment subworkflow which requires `--fasta` and `--somalier_sites`.
 
-### Mapping (`--skip_mapping_wf`)
+| Parameter        | Description                                                                                                                                                                        |
+| ---------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `fasta`          | Reference genome, either gzipped or uncompressed (e.g. [GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz](https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use)) |
+| `somalier_sites` | A VCF with known polymorphic sites from which sex will be inferred, if possible (e.g. [sites.hg38.vcg.gz](https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz))     |
 
-The majority of subworkflows depend on the mapping (alignment) subworkflow which requires `--fasta` and `--somalier_sites`.
+Turned off with `--skip_alignment`.
 
-| Parameter        | Description                                                                                                                                                                                                                                                                |
-| ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `fasta`          | Reference genome, either gzipped or uncompressed FASTA (e.g. [GRCh38_no_alt_analysis_set.fna.gz](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz)) |
-| `somalier_sites` | A VCF of known polymorphic sites (e.g. [sites.hg38.vcg.gz](https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz)), from which sex will be inferred if possible.                                                                                              |
+### QC
 
-### Aligned read QC (`--skip_aligned_read_qc`)
+This subworkflow depends on the alignment subworkflow, but requires no additional files.
 
-This subworkflow depends on the mapping subworkflow, but requires no additional files.
+Turned off with `--skip_qc`.
 
-### Assembly (`--skip_assembly_wf`)
+### Assembly
 
-This subworkflow contains both genome assembly and assembly variant calling. The assemblyt variant calling needs the sex of samples and for samples with unknown sex this is inferred from aligned reads, therefore it depends on the mapping subworkflow.
+This subworkflow contains both genome assembly and assembly variant calling. The assembly variant calling needs the sex of samples. For samples with unknown sex this is inferred with the help of the aligned reads. Therefore it depends on the alignment subworkflow. It requires a BED file with PARs.
 
-It requires a BED file with PAR regions.
+| Parameter     | Description                                                                                                                        |
+| ------------- | ---------------------------------------------------------------------------------------------------------------------------------- |
+| `par_regions` | A BED file with PAR regions (e.g. [GRCh38_PAR.bed](https://storage.googleapis.com/deepvariant/case-study-testdata/GRCh38_PAR.bed)) |
 
-| Parameter     | Description                                                                                                                       |
-| ------------- | --------------------------------------------------------------------------------------------------------------------------------- |
-| `par_regions` | A BED file with PAR regions (e.g. [GRCh38_PAR.bed](ttps://storage.googleapis.com/deepvariant/case-study-testdata/GRCh38_PAR.bed)) |
+!!!warning
+
+    Make sure chrY PAR is hard masked (masked with the letter N) in the reference genome you are using.
 
-> [!NOTE]
-> Make sure chrY PAR is hard masked in reference genome you are using.
+Turned off with `--skip_genome_assembly`.
 
-### Call paralogs (`--skip_call_paralogs`)
+### Call paralogs
 
 This subworkflow depends on the mapping subworkflow, but requires no additional files.
 
-> [!NOTE]
-> Only GRCh38 is supported.
+!!!warning
+
+    Only GRCh38 is supported.
+
+Turned off with `--skip_call_paralogs`.
 
-### Short variant calling (`--skip_short_variant_calling`)
+### SNV calling
 
-This subworkflow depends on the mapping subworkflow, and required the same PAR regions file as the assembly workflow.
+This subworkflow depends on the alignment subworkflow, and requires PARs.
 
 | Parameter     | Description                                                                                                                       |
 | ------------- | --------------------------------------------------------------------------------------------------------------------------------- |
 | `par_regions` | A BED file with PAR regions (e.g. [GRCh38_PAR.bed](ttps://storage.googleapis.com/deepvariant/case-study-testdata/GRCh38_PAR.bed)) |
 
-### CNV calling (`--skip_cnv_calling`)
+Turned off with `--skip_snv_calling`.
+
+### CNV calling
+
+This subworkflow depends on the alignment and SNV calling subworkflows, and requires the following additional files:
+
+| Parameter                  | Description                                                                                                                                                                                     |
+| -------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `hificnv_expected_xy_cn`   | Expected XY copy number regions for your reference genome (e.g. [expected_cn.hg38.XY.bed](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/expected_cn/expected_cn.hg38.XY.bed))     |
+| `hificnv_expected_xx_cn`   | Expected XX copy number regions for your reference genome (e.g. [expected_cn.hg38.XX.bed](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/expected_cn/expected_cn.hg38.XX.bed))     |
+| `hificnv_excluded_regions` | BED file specifying regions to exclude (e.g. [cnv.excluded_regions.hg38.bed.gz](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/excluded_regions/cnv.excluded_regions.hg38.bed.gz)) |
+
+Turned off with `--skip_cnv_calling`.
 
-This subworkflow depends on the mapping and short variant calling subworkflows, and requires the following additional files:
+### Phasing
 
-| Parameter         | Description                                                                                                                                                                                     |
-| ----------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `hificnv_xy`      | expected XY copy number regions for your reference genome (e.g. [expected_cn.hg38.XY.bed](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/expected_cn/expected_cn.hg38.XY.bed))     |
-| `hificnv_xx`      | expected XX copy number regions for your reference genome (e.g. [expected_cn.hg38.XX.bed](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/expected_cn/expected_cn.hg38.XX.bed))     |
-| `hificnv_exclude` | BED file specifying regions to exclude (e.g. [cnv.excluded_regions.hg38.bed.gz](https://github.com/PacificBiosciences/HiFiCNV/raw/main/data/excluded_regions/cnv.excluded_regions.hg38.bed.gz)) |
+This subworkflow phases variants and haplotags aligned BAM files, and such relies on the alignment and SNV calling subworkflows, but requires no additional files.
 
-### Phasing (`--skip_phasing_wf`)
+Turned off with `--skip_phasing`.
 
-This subworkflow phases variants and haplotags aligned BAM files, and such relies on the mapping and short variant calling subworkflows, but requires no additional files.
+### Methylation pileups
 
-### Methylation (`--skip_methylation_wf`)
+This subworkflow relies on alignment and short variant calling subworkflows, but requires no additional files.
 
-This subworkflow relies on mapping, short variant calling and phasing subworkflows, but requires no additional files.
+Turned off with `--skip_methylation_pileups`.
 
-### Repeat calling (`--skip_repeat_calling`)
+### Repeat calling
 
-This subworkflow requires haplotagged BAM files, and such relies on the mapping, short variant calling and phasing subworkflows, and requires the following additional files:
+This subworkflow requires haplotagged BAM files, and such relies on aligment, SNV calling and phasing subworkflows. It requires the following additional files:
 
-| Parameter      | Description                                                                                                                                                                                                                                                   |
-| -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `trgt_repeats` | a BED file with tandem repeats matching your reference genome (e.g. [pathogenic_repeats.hg38.bed](<[https://github.com/PacificBiosciences/trgt/tree/main/repeats](https://github.com/PacificBiosciences/trgt/raw/main/repeats/pathogenic_repeats.hg38.bed)>)) |
+| Parameter      | Description                                                                                                                                                                                 |
+| -------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `trgt_repeats` | a BED file with tandem repeats matching your reference genome (e.g. [pathogenic_repeats.hg38.bed](https://github.com/PacificBiosciences/trgt/raw/main/repeats/pathogenic_repeats.hg38.bed)) |
 
-### Repeat annotation (`--skip_repeat_annotation`)
+Turned off with `--skip_repeat_calling`.
 
-This subworkflow relies on the mapping, short variant calling, phasing and repeat calling subworkflows, and requires the following additional files:
+### Repeat annotation
 
-| Parameter         | Description                                                                                                                                                                           |
-| ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `variant_catalog` | a variant catalog matching your reference (e.g. [variant_catalog_grch38.json](https://github.com/Clinical-Genomics/stranger/raw/main/stranger/resources/variant_catalog_grch38.json)) |
+This subworkflow relies on the alignment, SNV calling, phasing and repeat calling subworkflows. It requires the following additional files:
 
-### SNV annotation (`--skip_snv_annotation`)
+| Parameter                 | Description                                                                                                                                                                                           |
+| ------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `stranger_repeat_catalog` | a variant catalog matching your reference (e.g. [stranger_repeat_catalog_grch38.json](https://github.com/Clinical-Genomics/stranger/raw/main/stranger/resources/stranger_repeat_catalog_grch38.json)) |
 
-This subworkflow relies on the mapping and short variant calling, and requires the following additional files:
+Turned off with `--skip_repeat_annotation`.
 
-<!-- TODO: score_config_snv, reduced_penetrance and variant_consequences_snv should link to real examples -->
+### SNV annotation
 
-| Parameter                  | Description                                                                                                                                                                                                                                                                                                                                                                   |
-| -------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `vep_cache`                | VEP cache matching your reference genome, either as a `.tar.gz` archive or path to a directory (e.g. [homo_sapiens_vep_110_GRCh38.tar.gz](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz))                                                                                                                                          |
-| `vep_plugins` <sup>1</sup> | A csv file with VEP plugin files, pLI and LoFtool are required. Example provided below.                                                                                                                                                                                                                                                                                       |
-| `snp_db` <sup>2</sup>      |  A csv file with annotation databases from ([`echtvar encode`](https://github.com/brentp/echtvar)) (e.g. [gnomad.v3.1.2.echtvar.popmax.v2.zip](https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download))                                                                                                                                                         |
-| `variant_consequences_snv` | A list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://ensembl.org/info/genome/variation/prediction/predicted_data.html) |
+This subworkflow relies on the alignment and SNV calling, and requires the following additional files:
 
-<sup>1</sup> Example file for input with `--vep_plugins`
+<!-- TODO: genmod_score_config_snvs, genmod_reduced_penetrance and variant_consequences_snvs should link to real examples -->
 
-- If running without `--skip_snv_annotation`, `--variant_consequences_snv` is also required (File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html)).
+| Parameter                            | Description                                                                                                                                                                                                                                                                                                                                                                   |
+| ------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `vep_cache`                          | VEP cache matching your reference genome, either as a `.tar.gz` archive or path to a directory (e.g. [homo_sapiens_vep_110_GRCh38.tar.gz](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz))                                                                                                                                          |
+| `vep_plugin_files` <sup>1</sup>      | A csv file with VEP plugin files, pLI and LoFtool are required. Example provided below.                                                                                                                                                                                                                                                                                       |
+| `echtvar_snv_databases` <sup>2</sup> | A csv file with annotation databases from [echtvar encode](https://github.com/brentp/echtvar) (e.g. [`gnomad.v3.1.2.echtvar.popmax.v2.zip`](https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download))                                                                                                                                                            |
+| `variant_consequences_snvs`          | A list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://ensembl.org/info/genome/variation/prediction/predicted_data.html) |
+
+<sup>1</sup> Example file for input with `--vep_plugin_files`
 
 ```
 vep_files
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/LoFtool.pm
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/dbNSFP.pm
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/plugin_config.txt
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_indel_-v1.3-.vcf.gz.tbi
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_indel_-v1.3-.vcf.gz
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/pLI_values.txt
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/pLI.pm
-https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/MaxEntScan.pm
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/LoFtool_scores.txt
 ```
 
-<sup>2</sup> Example file for input with `--vep_plugins`:
+<sup>2</sup> Example file for input with `--echtvar_snv_databases`:
 
 ```
 sample,file
@@ -242,25 +255,80 @@ gnomad,/path/to/gnomad.v3.1.2.echtvar.popmax.v2.zip
 cadd,/path/to/cadd.v1.6.hg38.zip
 ```
 
-> [!NOTE]
-> Optionally, to calcuate CADD scores for small indels, supply a path to a folder containing cadd annotations with `--cadd_resources` and prescored indels with `--cadd_prescored`. Equivalent of the `data/annotations/` and `data/prescored/` folders described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation). CADD scores for SNVs can be annotated through echvtvar and `--snp_db`.
+!!!tip
+
+    Optionally, to calcuate CADD scores for small indels, supply a path to a folder containing cadd annotations with `--cadd_resources` and prescored indels with `--cadd_prescored_indels`. Equivalent of the `data/annotations/` and `data/prescored/` folders described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation). CADD scores for SNVs can be annotated through echvtvar and `--echtvar_snv_databases`.
+
+Turned off with `--skip_snv_annotation`.
+
+### Rank SNVs and INDELs
 
-### Rank variants (`--skip_rank_variants`)
+This subworkflow ranks SNVs, and relies on the alignment, SNV calling and SNV annotation subworkflows. It requires the following additional files:
 
-This subworkflow relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files:
+| Parameter                   | Description                                                                                                                                                                                                                                                 |
+| --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `genmod_score_config_snvs`  |  Used by GENMOD when ranking variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini)                                                                                                           |
+| `genmod_reduced_penetrance` | A list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv) |
 
-| Parameter            | Description                                                                                                                                                                                                                                                  |
-| -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `score_config_snv`   |  Used by GENMOD when ranking variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini).                                                                                                           |
-| `reduced_penetrance` | A list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv)) |
+Turned off with `--skip_rank_variants`.
 
-### Other highlighted parameters
+### SV annotation
 
-- Limit SNV calling to regions in BED file (`--bed`).
-- By default SNV-calling is split into 13 parallel processes, this speeds up the variant calling significantly. Limit this by setting `--parallel_snv` to a different number.
-- By default the pipeline does not perform parallel alignment, but this can be changed by setting `--parallel_alignments` to split the alignment into multiple processes. This comes with some additional overhead, but speeds up the alignment significantly.
+This subworkflow relies on the alignment subworkflow, and requires the following additional files:
 
-### Reproducibility
+| Parameter                        | Description                                                           |
+| -------------------------------- | --------------------------------------------------------------------- |
+| `svdb_sv_databases` <sup>1</sup> | Csv file with databases (VCFs) used for structural variant annotation |
+
+<sup>1</sup> Example file for input with `--svdb_sv_databases`:
+
+```
+filename,in_freq_info_key,in_allele_count_info_key,out_freq_info_key,out_allele_count_info_key
+https://github.com/genomic-medicine-sweden/test-datasets/raw/b9ff54b59cdd39df5b6e278a30b08d94075a644c/reference/colorsdb.test_data.vcf.gz,AF,AC,colorsdb_af,colorsdb_ac
+```
+
+These databases could for example come from [CoLoRSdb](https://zenodo.org/records/13145123).
+
+Turned off with `--skip_sv_annotation`.
+
+### Rank SVs
+
+This subworkflow ranks SVs, and relies on the mapping, SV calling and SV annotation subworkflows, and requires the following additional files:
+
+| Parameter                   | Description                                                                                                                                                                                                                                                 |
+| --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `genmod_score_config_svs`   |  Used by GENMOD when ranking variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini)                                                                                                           |
+| `genmod_reduced_penetrance` | A list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv) |
+
+`--skip_rank_variants`.
+
+### Filter variants
+
+This subworkflow filters SNVs and SVs. It required at least the alignment and SNV calling workflows, but most of the time also the SNV annotation and ranking workflows.
+
+| Parameter                               | Description                                                                                                                                                               |
+| --------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `filter_variants_hgnc_ids` <sup>1</sup> |  Used by filter_vep to filter variants on HGNC IDs. Requires a tsv/csv file with a `hgnc_ids` column, that has one numerical HGNC ID per row, e.g. `4281` or `HGNC:4281`. |
+| `filter_snvs_expression`                | An expression that is passed to bcftools view to filter SNVs, e.g. `--filter_snvs_expression "-e 'INFO/AQ>60'"`                                                           |
+| `filter_svs_expression`                 | An expression that is passed to bcftools view to filter SVs, e.g.`--filter_snvs_expression "-e 'INFO/AQ>60'"`                                                             |
+
+<sup>1</sup> Example file for input with `--filter_variants_hgnc_ids`:
+
+```
+hgnc_id
+4865
+14150
+```
+
+Filtering of variants only happens if any of these three parameters is active.
+
+## Other highlighted parameters
+
+- Limit SNV calling to regions in BED file (`--target_bed`).
+- By default SNV-calling is split into 13 parallel processes, this speeds up the variant calling significantly. Change this by setting `--snv_calling_processes` to a different number.
+- By default the pipeline splits the input files into 8 pieces, performs parallel alignment and then merges the files. This can be changed to a different number with `--alignment_processes`, or turned off by supplying a value of 1. Parallel alignment comes with some additional overhead, but can speed up the pipeline significantly.
+
+## Reproducibility
 
 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
@@ -270,13 +338,15 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> [!TIP]
-> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+!!!tip
+
+    If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-> [!NOTE]
-> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+!!!note
+
+    These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
 
 ### `-profile`
 
@@ -349,14 +419,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
@@ -377,21 +439,12 @@ NXF_OPTS='-Xms1g -Xmx4g'
 
 ## Running the pipeline without internet access
 
-The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters).
-
-Contrary to the paragraph about [Nextflow](https://nf-co.re/docs/usage/offline#nextflow) on the page linked above, it is not possible to use the "-all" packaged version of Nextflow for this pipeline. The online version of Nextflow is necessary to support the necessary nextflow plugins. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly:
+### Download pipeline and containers
 
-```
-./nextflow plugin install nf-validation
-```
+The pipeline and container images can be downloaded using `nf-core download`, e.g.:
 
-Now you can transfer the `nextflow` binary as well as its directory `$HOME/.nextflow` to the system without Internet access, and use it there. It is necessary to use an explicit version of `nf-validation` offline, or Nextflow will check for the most recent version online. Find the version of nf-validation you downloaded in `$HOME/.nextflow/plugins`, then specify this version for `nf-validation` in your configuration file:
-
-```
-plugins {
-        // Set the plugin version explicitly, otherwise nextflow will look for the newest version online.
-        id 'nf-validation@1.1.3'
-}
+```bash
+nf-core download genomic-medicine-sweden/nallo -r 0.3.2
 ```
 
-This should go in your Nextflow confgiguration file, specified with `-c <YOURCONFIG>` when running the pipeline.
+The [offline section](https://nf-co.re/docs/usage/offline#nextflow) from the nf-core docs should be followed for more information about offline usage.
diff --git a/main.nf b/main.nf
index da4bb096..aab29291 100644
--- a/main.nf
+++ b/main.nf
@@ -6,9 +6,6 @@
     Github : https://github.com/genomic-medicine-sweden/nallo
 ----------------------------------------------------------------------------------------
 */
-
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -18,7 +15,6 @@ nextflow.enable.dsl = 2
 include { NALLO  } from './workflows/nallo'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_nallo_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_nallo_pipeline'
-
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_nallo_pipeline'
 
 /*
@@ -36,6 +32,7 @@ workflow GENOMICMEDICINESWEDEN_NALLO {
     samplesheet // channel: samplesheet read in from --input
 
     main:
+
     //
     // WORKFLOW: Run pipeline
     //
@@ -56,13 +53,11 @@ workflow GENOMICMEDICINESWEDEN_NALLO {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..418a2604
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,66 @@
+# based on: https://github.com/nf-cmgg/structural/blob/master/mkdocs.yml
+site_name: genomic-medicine-sweden/nallo
+repo_name: genomic-medicine-sweden/nallo
+repo_url: https://github.com/genomic-medicine-sweden/nallo
+site_url: https://genomic-medicine-sweden.github.io/nallo
+
+nav:
+  - Home: index.md
+  - Usage: usage.md
+  - Output: output.md
+  - Parameters: parameters.md
+  - Citations: CITATIONS.md
+
+theme:
+  name: material
+  icon:
+    logo: octicons/checklist-16
+    repo: fontawesome/brands/github
+  palette:
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to light mode
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/weather-night
+        name: Switch to dark mode
+  font:
+    text: Inter
+  features:
+    - content.code.annotate
+    - content.code.copy
+    - navigation.instant
+    - navigation.top
+    - navigation.tracking
+    - navigation.sections
+    - navigation.footer
+    - search.share
+    - toc.follow
+
+markdown_extensions:
+  - attr_list
+  - md_in_html
+  - admonition
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+
+extra:
+  version:
+    provider: mike
diff --git a/modules.json b/modules.json
index 94687dcd..0e060712 100644
--- a/modules.json
+++ b/modules.json
@@ -7,245 +7,298 @@
                 "nf-core": {
                     "bcftools/annotate": {
                         "branch": "master",
-                        "git_sha": "682f789f93070bd047868300dd018faf3d434e7c",
-                        "installed_by": ["modules"]
+                        "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890",
+                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "bcftools/merge": {
+                    "bcftools/norm": {
                         "branch": "master",
-                        "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "bcftools/norm": {
+                    "bcftools/pluginsplit": {
                         "branch": "master",
-                        "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "bcftools/pluginsplit": {
+                    "bcftools/query": {
                         "branch": "master",
-                        "git_sha": "c5abf7acbb2943bf09f4025cacbbcc2bc2292637",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bcftools/reheader": {
                         "branch": "master",
-                        "git_sha": "682f789f93070bd047868300dd018faf3d434e7c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bedtools/merge": {
                         "branch": "master",
-                        "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bedtools/sort": {
                         "branch": "master",
-                        "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cadd": {
                         "branch": "master",
-                        "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cadd/cadd.diff"
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
                         "installed_by": ["modules"]
                     },
-                    "deepvariant": {
+                    "deepvariant/rundeepvariant": {
                         "branch": "master",
-                        "git_sha": "a7e8b8afd4fa82f20d745fa778bfdbf39c1f7efb",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "ensemblvep/vep": {
+                    "deepvariant/vcfstatsreport": {
+                        "branch": "master",
+                        "git_sha": "2f9a5431355897e299cb41928c45f51ea8410c42",
+                        "installed_by": ["modules"]
+                    },
+                    "ensemblvep/filtervep": {
                         "branch": "master",
-                        "git_sha": "e1938f8ecb13b9b82ff488d4b35269c84aa965e8",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
                         "installed_by": ["modules"]
                     },
+                    "ensemblvep/vep": {
+                        "branch": "master",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
+                    },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
+                        "git_sha": "97321eded31a12598837a476d3615300af413bb7",
                         "installed_by": ["modules"]
                     },
                     "genmod/annotate": {
                         "branch": "master",
-                        "git_sha": "043f1164b94bcaf7b9810db243a8c37c66298077",
+                        "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c",
                         "installed_by": ["modules"]
                     },
                     "genmod/compound": {
                         "branch": "master",
-                        "git_sha": "89fe39b745da3dca14ad1a361784812ea3aa3a43",
+                        "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c",
                         "installed_by": ["modules"]
                     },
                     "genmod/models": {
                         "branch": "master",
-                        "git_sha": "043f1164b94bcaf7b9810db243a8c37c66298077",
+                        "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6",
                         "installed_by": ["modules"]
                     },
                     "genmod/score": {
                         "branch": "master",
-                        "git_sha": "043f1164b94bcaf7b9810db243a8c37c66298077",
+                        "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6",
                         "installed_by": ["modules"]
                     },
                     "gfastats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "glnexus": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/glnexus/glnexus.diff"
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "hifiasm": {
                         "branch": "master",
-                        "git_sha": "aecb06fcdb995ff3e3df7c7a1fd119367d6d1996",
+                        "git_sha": "daa15d5226111e10ca95c0d4a85fa6bd11a08a01",
+                        "installed_by": ["modules"]
+                    },
+                    "longphase/haplotag": {
+                        "branch": "master",
+                        "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c",
+                        "installed_by": ["modules"]
+                    },
+                    "longphase/phase": {
+                        "branch": "master",
+                        "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "modkit/pileup": {
                         "branch": "master",
-                        "git_sha": "e29c9dda946de3c4d310d0b3f75664f0f3d5a842",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "paraphase": {
                         "branch": "master",
-                        "git_sha": "54b51b69634128ca63568e87387ab1140a5c9410",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/fastq": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/import": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3",
-                        "installed_by": ["modules"]
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/merge/samtools-merge.diff"
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
-                        "installed_by": ["modules"]
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
-                    "sniffles": {
+                    "severus": {
                         "branch": "master",
-                        "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf",
+                        "git_sha": "8a36181859504560ef333c299f6773c7b99a801f",
                         "installed_by": ["modules"]
                     },
+                    "sniffles": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/sniffles/sniffles.diff"
+                    },
                     "somalier/extract": {
                         "branch": "master",
-                        "git_sha": "458c882987320e27fc90723ec96c127a243a5497",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/somalier/extract/somalier-extract.diff"
                     },
                     "somalier/relate": {
                         "branch": "master",
-                        "git_sha": "458c882987320e27fc90723ec96c127a243a5497",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/somalier/relate/somalier-relate.diff"
                     },
                     "splitubam": {
                         "branch": "master",
-                        "git_sha": "d12bb6cdcd22ef8f26803a6a55e918ac017176e8",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "stranger": {
                         "branch": "master",
-                        "git_sha": "4806239588f35d27a95b187b4000d80e15152022",
+                        "git_sha": "26cdbf29e76695c7fd85e42e0015c7e96f979fe9",
+                        "installed_by": ["modules"]
+                    },
+                    "svdb/merge": {
+                        "branch": "master",
+                        "git_sha": "a8ad84b7ee0cda0b001490e95d9ed277e687e368",
+                        "installed_by": ["modules"]
+                    },
+                    "svdb/query": {
+                        "branch": "master",
+                        "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c",
+                        "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "untar": {
+                    "trgt/genotype": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "484afd16770cf3c466a6c385e33746c877656663",
                         "installed_by": ["modules"]
+                    },
+                    "trgt/merge": {
+                        "branch": "master",
+                        "git_sha": "8f77dd07042aef4eb19ea7fa91496a41975299b0",
+                        "installed_by": ["modules"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/untar/untar.diff"
                     }
                 }
             },
@@ -253,17 +306,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/local/add_found_in_tag/environment.yml
similarity index 80%
rename from modules/nf-core/bcftools/merge/environment.yml
rename to modules/local/add_found_in_tag/environment.yml
index 51f1fb75..a8a985fa 100644
--- a/modules/nf-core/bcftools/merge/environment.yml
+++ b/modules/local/add_found_in_tag/environment.yml
@@ -1,4 +1,4 @@
-name: bcftools_merge
+name: add_found_in_tag
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/local/add_found_in_tag/main.nf b/modules/local/add_found_in_tag/main.nf
new file mode 100644
index 00000000..ff31cdeb
--- /dev/null
+++ b/modules/local/add_found_in_tag/main.nf
@@ -0,0 +1,96 @@
+process ADD_FOUND_IN_TAG {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
+        'biocontainers/bcftools:1.20--h8b25389_0' }"
+
+    input:
+    tuple val(meta), path(vcf, stageAs: "?/*"), path(index, stageAs: "?/*")
+    val(variant_caller)
+
+    output:
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args2.contains('--output-type b') || args2.contains('-Ob') ? 'bcf.gz' :
+                    args2.contains('--output-type u') || args2.contains('-Ou') ? 'bcf' :
+                    args2.contains('--output-type z') || args2.contains('-Oz') ? 'vcf.gz' :
+                    args2.contains('--output-type v') || args2.contains('-Ov') ? 'vcf' :
+                    'vcf'
+
+    """
+    bcftools view \\
+        $args \\
+        --threads $task.cpus \\
+        $vcf |\\
+    awk '
+        # Print all existing header lines
+        /^##/ {
+            print;
+            next;
+        }
+
+        # Add a INFO header line before the #CHROM line, then print the #CHROM line
+        /^#CHROM/ {
+            printf("##INFO=<ID=FOUND_IN,Number=1,Type=String,Description=\\"Program that called the variant\\">\\n");
+            print;
+            next;
+        }
+
+        # Then for all other lines, append FOUND_IN=variant_caller to the INFO field (column 8)
+        {
+            OFS="\\t";
+            \$8 = sprintf("%s;FOUND_IN=${variant_caller}", \$8 );
+            print;
+        }
+    ' |\\
+    bcftools view \\
+        $args2 \\
+        --threads $task.cpus \\
+        --output ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        busybox_awk: \$(awk 2>&1 | sed -n 's/.*v\\([^ ]*\\) (.*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args2.contains('--output-type b') || args2.contains('-Ob') ? 'bcf.gz' :
+                    args2.contains('--output-type u') || args2.contains('-Ou') ? 'bcf' :
+                    args2.contains('--output-type z') || args2.contains('-Oz') ? "vcf.gz" :
+                    args2.contains('--output-type v') || args2.contains('-Ov') ? 'vcf' :
+                    'vcf'
+    def index = args2.contains('--write-index=tbi') || args2.contains('-W=tbi') ? 'tbi' :
+                args2.contains('--write-index=csi') || args2.contains("-W=csi") ? 'csi' :
+                args2.contains('--write-index') || args2.contains("-W") ? 'csi' :
+                ''
+    def create_cmd = extension.endsWith('.gz') ? "echo '' | gzip >" : 'touch'
+    def create_index = extension.endsWith('.gz') && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ''
+
+    """
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        busybox_awk: \$(awk 2>&1 | sed -n 's/.*v\\([^ ]*\\) (.*/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/add_found_in_tag/tests/main.nf.test b/modules/local/add_found_in_tag/tests/main.nf.test
new file mode 100644
index 00000000..02385503
--- /dev/null
+++ b/modules/local/add_found_in_tag/tests/main.nf.test
@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process ADD_FOUND_IN_TAG"
+    script "../main.nf"
+    process "ADD_FOUND_IN_TAG"
+
+    tag "modules"
+    tag "modules_local"
+    tag "bcftools"
+    tag "add_found_in_tag"
+
+    test("sarscov2 - [vcf, []], variant_caller") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'out', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = 'variant_caller'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.vcf.get(0).get(1)).readLines().any { it.contains("FOUND_IN=variant_caller") } },
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, []], variant_caller -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'out', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = 'variant_caller'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/add_found_in_tag/tests/main.nf.test.snap b/modules/local/add_found_in_tag/tests/main.nf.test.snap
new file mode 100644
index 00000000..90deb557
--- /dev/null
+++ b/modules/local/add_found_in_tag/tests/main.nf.test.snap
@@ -0,0 +1,382 @@
+{
+    "sarscov2 - [vcf, []], variant_caller": {
+        "content": [
+            "7ce88babfa8801b2a913faf40c6f7edd",
+            [
+                "versions.yml:md5,5d810c4fbc154928fabfe136fad38704"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T09:33:11.23710858"
+    },
+    "sarscov2 - [vcf, []], variant_caller -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": [
+                                [
+                                    [
+                                        "HG002_Revio_phased.bam:md5,64e1d1ed3d180589193c13f2c94d1098",
+                                        "HG002_Revio_phased.bam.bai:md5,bb768f48be5144262c0b713ef183d152"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary:md5,e4da3107f2421d42c6e2f59bff4e47d9",
+                                            "HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz:md5,eff16bf92abff02c36cceb2eb5a9871c",
+                                            "HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary:md5,bf908610472e602fd986b9d4a4d58b9e",
+                                            "HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz:md5,e28c886baffe24c1a2972a1d95b1b250"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.dip.bed:md5,4e3cde029bceaa9363402e997f12f280",
+                                            "HG002_Revio.dip.vcf.gz:md5,9259613d7b01347b2d817d4e547c4203",
+                                            "HG002_Revio.hap1.bam:md5,5c739e8b3c2f659c3847498848280bbf",
+                                            "HG002_Revio.hap1.bam.bai:md5,a57472fa9365470db09f5ea8c7a7420a",
+                                            "HG002_Revio.hap1.bed:md5,3d75c9538e748a7672b934bdbde90df3",
+                                            "HG002_Revio.hap1.paf.gz:md5,46a3056ecd833d9a932c53fc46a3cafc",
+                                            "HG002_Revio.hap1.sam.gz:md5,0a161b44c29c0581ada87fee50be38c2",
+                                            "HG002_Revio.hap1.var.gz:md5,173218f6c3f5f067e0932a8331f12e3d",
+                                            "HG002_Revio.hap2.bam:md5,df63e7bb5dcee6ca5e731272dad0eb99",
+                                            "HG002_Revio.hap2.bam.bai:md5,ed8184223edea0297c7f9283ea7927bf",
+                                            "HG002_Revio.hap2.bed:md5,9ac411d49f08a8ec70e4792890e9faf9",
+                                            "HG002_Revio.hap2.paf.gz:md5,a99e451e4af96a7ab120cedd49eea618",
+                                            "HG002_Revio.hap2.sam.gz:md5,410acad899eda2f0a4a3e1eb4acf81cb",
+                                            "HG002_Revio.hap2.var.gz:md5,53dc16fc893a529a95067da161b4dad6",
+                                            "HG002_Revio.pair.vcf.gz:md5,a390558ab50ce0dc9efec070b1c70c22"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.HG002_Revio.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
+                                            "HG002_Revio.HG002_Revio.depth.bw:md5,20757c985f4713b8568dee05765db701",
+                                            "HG002_Revio.HG002_Revio.maf.bw:md5,4699d7a664277863f06eb48c3cba3c41",
+                                            "HG002_Revio.HG002_Revio.vcf.gz:md5,771f7d9ecbd161dedfbdd053ceff0d52",
+                                            "HG002_Revio.HG002_Revio.vcf.gz.tbi:md5,65d6930f79e626a5542091b7a419dc2b",
+                                            "HG002_Revio.log:md5,3b47302d7e8e0ffac4841123de74ffb3"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                
+                                            ],
+                                            [
+                                                
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "HG002_Revio.paraphase.bam:md5,839cab6fb9b453b36975e9ab650d2552",
+                                        "HG002_Revio.paraphase.bam.bai:md5,7146463306700bc589b4085c3404bac3",
+                                        "HG002_Revio.paraphase.json:md5,03ba9306a2bea70a817e4b2ef32d55b4",
+                                        [
+                                            "HG002_Revio_hba.vcf.gz:md5,fb0207f30c5bb0e3beba699e147feed9",
+                                            "HG002_Revio_hba.vcf.gz.tbi:md5,63656171e041cf226e8b312c3e989eee"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    "test_single.ped:md5,bd5cec27ba7337a85cf98e787131e2b5"
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "HG002_Revio_phased.vcf.gz:md5,cde30af0e4f160e91b9db0fcebebc2d1",
+                                                "HG002_Revio_phased.vcf.gz.tbi:md5,3e2fc64bb2f893b44dcf24817b4632f3"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_stats.blocks.tsv:md5,eaf8f60522034f52b3a45ced6ebed2ea",
+                                                "HG002_Revio_stats.stats.tsv:md5,b571fcb3ef8a9e7921dd2824cfc1f549"
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    "nf_core_pipeline_software_mqc_versions.yml:md5,3675babbfa3ff94ad52a8d090e42545e",
+                                    "params_2024-09-20_14-33-35.json:md5,ef85e454ae8828ddf71282d9aa407fb2"
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                                                "HG002_Revio_cramino_aligned_phased.txt:md5,3af7900149aa0b16e1f858feed041aaa"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                                                "HG002_Revio_cramino_aligned.txt:md5,10dc53594d12a53b793f8c8d4382b1fb"
+                                            ]
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            "HG002_Revio.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
+                                            "HG002_Revio.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
+                                            "HG002_Revio.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
+                                            "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
+                                            "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab"
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            [
+                                                "test_single.html:md5,d05e0eceb70ada3a0c25f99a16ad1889",
+                                                "test_single.pairs.tsv:md5,4a0988fc3c0fe5cfd5dd205fe6755595",
+                                                "test_single.samples.tsv:md5,1685dc6cb8c6b9806ca636662980d686"
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio_fastqc.html:md5,0337b9b2bb1368340c79624051d97363",
+                                            "HG002_Revio_fastqc.zip:md5,0b4dde7cf60185c165e61b689f246787"
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            "HG002_PacBio_Revio.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "test_single_sniffles.vcf.gz:md5,8386b2d30b0e77a644f26c820013df3f",
+                                                "test_single_sniffles.vcf.gz.tbi:md5,6fd9ceb01d7baec1b96ecb3b29583e0d"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_sniffles.snf:md5,b2d5a63bb00cabcb2527d361721f6fa1",
+                                                "HG002_Revio_sniffles.vcf.gz:md5,9b69d2d3f79130b6f483d12855ab07fa",
+                                                "HG002_Revio_sniffles.vcf.gz.tbi:md5,4d5ed6747851d968a0b9b51d0e3558b1"
+                                            ]
+                                        ]
+                                    ]
+                                ]
+                            ],
+                            "single_end": false
+                        },
+                        "out.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,5d810c4fbc154928fabfe136fad38704"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": [
+                                [
+                                    [
+                                        "HG002_Revio_phased.bam:md5,64e1d1ed3d180589193c13f2c94d1098",
+                                        "HG002_Revio_phased.bam.bai:md5,bb768f48be5144262c0b713ef183d152"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary:md5,e4da3107f2421d42c6e2f59bff4e47d9",
+                                            "HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz:md5,eff16bf92abff02c36cceb2eb5a9871c",
+                                            "HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary:md5,bf908610472e602fd986b9d4a4d58b9e",
+                                            "HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz:md5,e28c886baffe24c1a2972a1d95b1b250"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.dip.bed:md5,4e3cde029bceaa9363402e997f12f280",
+                                            "HG002_Revio.dip.vcf.gz:md5,9259613d7b01347b2d817d4e547c4203",
+                                            "HG002_Revio.hap1.bam:md5,5c739e8b3c2f659c3847498848280bbf",
+                                            "HG002_Revio.hap1.bam.bai:md5,a57472fa9365470db09f5ea8c7a7420a",
+                                            "HG002_Revio.hap1.bed:md5,3d75c9538e748a7672b934bdbde90df3",
+                                            "HG002_Revio.hap1.paf.gz:md5,46a3056ecd833d9a932c53fc46a3cafc",
+                                            "HG002_Revio.hap1.sam.gz:md5,0a161b44c29c0581ada87fee50be38c2",
+                                            "HG002_Revio.hap1.var.gz:md5,173218f6c3f5f067e0932a8331f12e3d",
+                                            "HG002_Revio.hap2.bam:md5,df63e7bb5dcee6ca5e731272dad0eb99",
+                                            "HG002_Revio.hap2.bam.bai:md5,ed8184223edea0297c7f9283ea7927bf",
+                                            "HG002_Revio.hap2.bed:md5,9ac411d49f08a8ec70e4792890e9faf9",
+                                            "HG002_Revio.hap2.paf.gz:md5,a99e451e4af96a7ab120cedd49eea618",
+                                            "HG002_Revio.hap2.sam.gz:md5,410acad899eda2f0a4a3e1eb4acf81cb",
+                                            "HG002_Revio.hap2.var.gz:md5,53dc16fc893a529a95067da161b4dad6",
+                                            "HG002_Revio.pair.vcf.gz:md5,a390558ab50ce0dc9efec070b1c70c22"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio.HG002_Revio.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
+                                            "HG002_Revio.HG002_Revio.depth.bw:md5,20757c985f4713b8568dee05765db701",
+                                            "HG002_Revio.HG002_Revio.maf.bw:md5,4699d7a664277863f06eb48c3cba3c41",
+                                            "HG002_Revio.HG002_Revio.vcf.gz:md5,771f7d9ecbd161dedfbdd053ceff0d52",
+                                            "HG002_Revio.HG002_Revio.vcf.gz.tbi:md5,65d6930f79e626a5542091b7a419dc2b",
+                                            "HG002_Revio.log:md5,3b47302d7e8e0ffac4841123de74ffb3"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                
+                                            ],
+                                            [
+                                                
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "HG002_Revio.paraphase.bam:md5,839cab6fb9b453b36975e9ab650d2552",
+                                        "HG002_Revio.paraphase.bam.bai:md5,7146463306700bc589b4085c3404bac3",
+                                        "HG002_Revio.paraphase.json:md5,03ba9306a2bea70a817e4b2ef32d55b4",
+                                        [
+                                            "HG002_Revio_hba.vcf.gz:md5,fb0207f30c5bb0e3beba699e147feed9",
+                                            "HG002_Revio_hba.vcf.gz.tbi:md5,63656171e041cf226e8b312c3e989eee"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    "test_single.ped:md5,bd5cec27ba7337a85cf98e787131e2b5"
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "HG002_Revio_phased.vcf.gz:md5,cde30af0e4f160e91b9db0fcebebc2d1",
+                                                "HG002_Revio_phased.vcf.gz.tbi:md5,3e2fc64bb2f893b44dcf24817b4632f3"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_stats.blocks.tsv:md5,eaf8f60522034f52b3a45ced6ebed2ea",
+                                                "HG002_Revio_stats.stats.tsv:md5,b571fcb3ef8a9e7921dd2824cfc1f549"
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    "nf_core_pipeline_software_mqc_versions.yml:md5,3675babbfa3ff94ad52a8d090e42545e",
+                                    "params_2024-09-20_14-33-35.json:md5,ef85e454ae8828ddf71282d9aa407fb2"
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                                                "HG002_Revio_cramino_aligned_phased.txt:md5,3af7900149aa0b16e1f858feed041aaa"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                                                "HG002_Revio_cramino_aligned.txt:md5,10dc53594d12a53b793f8c8d4382b1fb"
+                                            ]
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            "HG002_Revio.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
+                                            "HG002_Revio.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
+                                            "HG002_Revio.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
+                                            "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
+                                            "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab"
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            [
+                                                "test_single.html:md5,d05e0eceb70ada3a0c25f99a16ad1889",
+                                                "test_single.pairs.tsv:md5,4a0988fc3c0fe5cfd5dd205fe6755595",
+                                                "test_single.samples.tsv:md5,1685dc6cb8c6b9806ca636662980d686"
+                                            ]
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            "HG002_Revio_fastqc.html:md5,0337b9b2bb1368340c79624051d97363",
+                                            "HG002_Revio_fastqc.zip:md5,0b4dde7cf60185c165e61b689f246787"
+                                        ]
+                                    ],
+                                    [
+                                        [
+                                            "HG002_PacBio_Revio.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b"
+                                        ]
+                                    ]
+                                ],
+                                [
+                                    [
+                                        [
+                                            [
+                                                "test_single_sniffles.vcf.gz:md5,8386b2d30b0e77a644f26c820013df3f",
+                                                "test_single_sniffles.vcf.gz.tbi:md5,6fd9ceb01d7baec1b96ecb3b29583e0d"
+                                            ]
+                                        ],
+                                        [
+                                            [
+                                                "HG002_Revio_sniffles.snf:md5,b2d5a63bb00cabcb2527d361721f6fa1",
+                                                "HG002_Revio_sniffles.vcf.gz:md5,9b69d2d3f79130b6f483d12855ab07fa",
+                                                "HG002_Revio_sniffles.vcf.gz.tbi:md5,4d5ed6747851d968a0b9b51d0e3558b1"
+                                            ]
+                                        ]
+                                    ]
+                                ]
+                            ],
+                            "single_end": false
+                        },
+                        "out.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5d810c4fbc154928fabfe136fad38704"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T09:33:18.256743972"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/add_found_in_tag/tests/tags.yml b/modules/local/add_found_in_tag/tests/tags.yml
new file mode 100644
index 00000000..9d5792cf
--- /dev/null
+++ b/modules/local/add_found_in_tag/tests/tags.yml
@@ -0,0 +1,2 @@
+add_found_in_tag:
+  - "modules/local/add_found_in_tag/**"
diff --git a/modules/local/add_most_severe_consequence.nf b/modules/local/add_most_severe_consequence.nf
index 0c572811..26a4fce3 100644
--- a/modules/local/add_most_severe_consequence.nf
+++ b/modules/local/add_most_severe_consequence.nf
@@ -1,6 +1,6 @@
 process ADD_MOST_SEVERE_CSQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -9,11 +9,11 @@ process ADD_MOST_SEVERE_CSQ {
 
     input:
     tuple val(meta), path(vcf)
-    path (variant_consequences)
+    tuple val(meta2), path (variant_consequences)
 
     output:
-    tuple val(meta), path("*.vcf")        , emit: vcf
-    path "versions.yml"                   , emit: versions
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,12 +21,17 @@ process ADD_MOST_SEVERE_CSQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$vcf" == "${prefix}.vcf" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
-    add_most_severe_consequence.py --file_in ${vcf} --file_out ${prefix}.vcf --variant_csq ${variant_consequences}
+    add_most_severe_consequence.py \\
+        --file_in ${vcf} \\
+        --file_out ${prefix}.vcf \\
+        --variant_csq ${variant_consequences}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_consequence: v1.0
+        add_most_severe_consequence: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
@@ -38,7 +43,7 @@ process ADD_MOST_SEVERE_CSQ {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_consequence: v1.0
+        add_most_severe_consequence: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/add_most_severe_pli.nf b/modules/local/add_most_severe_pli.nf
index f2975a22..16286b49 100644
--- a/modules/local/add_most_severe_pli.nf
+++ b/modules/local/add_most_severe_pli.nf
@@ -1,6 +1,6 @@
 process ADD_MOST_SEVERE_PLI {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -11,8 +11,8 @@ process ADD_MOST_SEVERE_PLI {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.vcf")  , emit: vcf
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,12 +20,16 @@ process ADD_MOST_SEVERE_PLI {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$vcf" == "${prefix}.vcf" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
-    add_most_severe_pli.py --file_in ${vcf} --file_out ${prefix}.vcf
+    add_most_severe_pli.py \\
+        --file_in ${vcf} \\
+        --file_out ${prefix}.vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_pli: v1.0
+        add_most_severe_pli: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
@@ -37,7 +41,7 @@ process ADD_MOST_SEVERE_PLI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        add_most_severe_pli: v1.0
+        add_most_severe_pli: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/create_pedigree_file.nf b/modules/local/create_pedigree_file/main.nf
similarity index 66%
rename from modules/local/create_pedigree_file.nf
rename to modules/local/create_pedigree_file/main.nf
index 18480df5..37d9a0c1 100644
--- a/modules/local/create_pedigree_file.nf
+++ b/modules/local/create_pedigree_file/main.nf
@@ -1,5 +1,5 @@
 process CREATE_PEDIGREE_FILE {
-    tag "${project}"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "conda-forge::python=3.8.3"
@@ -8,17 +8,20 @@ process CREATE_PEDIGREE_FILE {
         'biocontainers/python:3.8.3' }"
 
     input:
-    tuple val(project), val(samples)
+    tuple val(meta), val(sample_metas)
 
     output:
-    tuple val(project), path("*.ped"), emit: ped
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.ped"), emit: ped
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def out   = new File(project + ".ped")
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def samples = (sample_metas.collect().size() > 1) ? sample_metas.sort{ a, b ->
+        // First sort on family_id, then on sample id
+        a.family_id <=> b.family_id ?: a.id <=> b.id } : sample_metas
     outfile_text = ['#family_id', 'sample_id', 'father', 'mother', 'sex', 'phenotype'].join('\\t')
     def samples_list = []
     for(int i = 0; i<samples.size(); i++) {
@@ -29,22 +32,23 @@ process CREATE_PEDIGREE_FILE {
         }
     }
     """
-    echo -e "$outfile_text" >${project}.ped
+    echo -e "$outfile_text" > ${prefix}.ped
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        create_pedigree_file: v1.0
+        create_pedigree_file: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
 
     stub:
+    def prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${project}.ped
+    touch ${prefix}.ped
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        create_pedigree_file: v1.0
+        create_pedigree_file: 1.0
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/create_pedigree_file/tests/main.nf.test b/modules/local/create_pedigree_file/tests/main.nf.test
new file mode 100644
index 00000000..1667d5bf
--- /dev/null
+++ b/modules/local/create_pedigree_file/tests/main.nf.test
@@ -0,0 +1,67 @@
+nextflow_process {
+
+    name "Test Process CREATE_PEDIGREE_FILE"
+    script "../main.nf"
+    process "CREATE_PEDIGREE_FILE"
+
+    tag "modules"
+    tag "modules_local"
+    tag "create_pedigree_file"
+
+    test("create_pedigree_file - one sample") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [ 'project',
+                    [
+                        [id:'HG002.Revio', family_id:'family', paternal_id:0, maternal_id:0, sex:0, phenotype:2, project:'project', n_files:1, single_end:true]
+                    ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.ped.get(0).get(1)).readLines(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("create_pedigree_file - multiple samples") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [ 'test',
+                    [
+                        [id:'HG002_Revio_AB', family_id:'FAM2', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:1, single_end:true],
+                        [id:'HG002_Revio_AA', family_id:'FAM2', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:1, single_end:true],
+                        [id:'HG002_Revio_B', family_id:'FAM1', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:2, single_end:true],
+                        [id:'HG002_Revio_A', family_id:'FAM1', paternal_id:0, maternal_id:0, sex:0, phenotype:2, project:'test', n_files:1, single_end:true],
+                        [id:'HG002_Revio_B', family_id:'FAM1', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:2, single_end:true]
+                    ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.ped.get(0).get(1)).readLines(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/local/create_pedigree_file/tests/main.nf.test.snap b/modules/local/create_pedigree_file/tests/main.nf.test.snap
new file mode 100644
index 00000000..38ecf6ba
--- /dev/null
+++ b/modules/local/create_pedigree_file/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "create_pedigree_file - one sample": {
+        "content": [
+            [
+                "#family_id\tsample_id\tfather\tmother\tsex\tphenotype",
+                "family\tHG002.Revio\t0\t0\t0\t2"
+            ],
+            [
+                "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-04T16:16:12.293913485"
+    },
+    "create_pedigree_file - multiple samples": {
+        "content": [
+            [
+                "#family_id\tsample_id\tfather\tmother\tsex\tphenotype",
+                "FAM1\tHG002_Revio_A\t0\t0\t0\t2",
+                "FAM1\tHG002_Revio_B\t0\t0\t0\t1",
+                "FAM2\tHG002_Revio_AA\t0\t0\t0\t1",
+                "FAM2\tHG002_Revio_AB\t0\t0\t0\t1"
+            ],
+            [
+                "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-04T16:16:19.916570689"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/create_samples_file/main.nf b/modules/local/create_samples_file/main.nf
new file mode 100644
index 00000000..b4847ed8
--- /dev/null
+++ b/modules/local/create_samples_file/main.nf
@@ -0,0 +1,44 @@
+process CREATE_SAMPLES_FILE {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "anaconda::gawk=5.1.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
+        'biocontainers/gawk:5.1.0' }"
+
+    input:
+    tuple val(meta), path(txt)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: samples
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$txt" == "${prefix}.txt") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    awk '{print \$1,"${meta.id}"}' ${txt} > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/create_samples_file/tests/main.nf.test b/modules/local/create_samples_file/tests/main.nf.test
new file mode 100644
index 00000000..38c558b4
--- /dev/null
+++ b/modules/local/create_samples_file/tests/main.nf.test
@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process CREATE_SAMPLES_FILE"
+    script "../main.nf"
+    process "CREATE_SAMPLES_FILE"
+
+    tag "modules"
+    tag "modules_local"
+    tag "create_samples_file"
+
+    config "./nextflow.config"
+
+    test("create_samples_file") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of('test_vcf_file_sample')
+                    .collectFile(name: 'test.txt')
+                    .map { file -> [ [ id: 'test' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("create_samples_file -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of('test_vcf_file_sample')
+                    .collectFile(name: 'test.txt')
+                    .map { file -> [ [ id: 'test' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/local/create_samples_file/tests/main.nf.test.snap b/modules/local/create_samples_file/tests/main.nf.test.snap
new file mode 100644
index 00000000..5579fc68
--- /dev/null
+++ b/modules/local/create_samples_file/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "create_samples_file -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "samples_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ef72b0fd7e245e40b0ce6d409e218689"
+                ],
+                "samples": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "samples_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ef72b0fd7e245e40b0ce6d409e218689"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-11T18:56:06.026507892"
+    },
+    "create_samples_file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "samples_file.txt:md5,41e40eee31c3003c213685c180f52c25"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ef72b0fd7e245e40b0ce6d409e218689"
+                ],
+                "samples": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "samples_file.txt:md5,41e40eee31c3003c213685c180f52c25"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ef72b0fd7e245e40b0ce6d409e218689"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-11T18:55:18.906428667"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/create_samples_file/tests/nextflow.config b/modules/local/create_samples_file/tests/nextflow.config
new file mode 100644
index 00000000..f65fe04c
--- /dev/null
+++ b/modules/local/create_samples_file/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'CREATE_SAMPLES_FILE' {
+        ext.prefix = 'samples_file'
+    }
+}
diff --git a/modules/local/fqcrs/Dockerfile b/modules/local/fqcrs/Dockerfile
deleted file mode 100644
index 955356d5..00000000
--- a/modules/local/fqcrs/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-# syntax=docker/dockerfile:1
-FROM ubuntu:22.04
-
-RUN apt-get update && apt-get install -y procps sed zstd && rm -rf /var/lib/apt/lists/*
-# install app
-COPY fqcrs /usr/bin/fqcrs
-
-# final configuration
-ENV FLASK_APP=fqcrs
diff --git a/modules/local/fqcrs/main.nf b/modules/local/fqcrs/main.nf
deleted file mode 100644
index 64162695..00000000
--- a/modules/local/fqcrs/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-process FQCRS {
-    tag "$meta.id"
-    label 'process_single'
-
-    container "docker.io/fellen31/fqcrs:0.1.0"
-    // Add verion manually
-    def fqcrs_version = '0.1.0'
-
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "FQCRS module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("${prefix}.tsv.zst"), emit: fqc
-    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}"
-
-    """
-    zcat ${reads} | fqcrs | zstd -c > ${prefix}.tsv.zst
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fqcrs: \$(echo "$fqcrs_version" )
-    END_VERSIONS
-    """
-}
-
diff --git a/modules/local/hiphase/main.nf b/modules/local/hiphase/main.nf
index 44b5d4bf..3de4359a 100644
--- a/modules/local/hiphase/main.nf
+++ b/modules/local/hiphase/main.nf
@@ -42,7 +42,7 @@ process HIPHASE {
         vcfInputs.add('--vcf')
         vcfInputs.add(vcf)
         vcfOutputs.add('--output-vcf')
-        vcfOutputs.add("${prefix}.vcf.gz")
+        vcfOutputs.add("${prefix}_phased.vcf.gz")
 
         vcfNames.add(vcf.getName())
     }
@@ -58,7 +58,7 @@ process HIPHASE {
 
         if(output_bam) {
             bamOutputs.add('--output-bam')
-            bamOutputs.add("${prefix}.bam")
+            bamOutputs.add("${prefix}_haplotagged.bam")
         }
     }
 
diff --git a/modules/local/pacbio/hificnv/main.nf b/modules/local/pacbio/hificnv/main.nf
index 31131ab6..9046dca8 100644
--- a/modules/local/pacbio/hificnv/main.nf
+++ b/modules/local/pacbio/hificnv/main.nf
@@ -2,14 +2,17 @@ process HIFICNV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::hificnv=0.1.7"
-    container "quay.io/biocontainers/hificnv:0.1.7--h9ee0642_0"
-
+    conda "bioconda::hificnv=1.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hificnv:1.0.0--h9ee0642_0' :
+        'quay.io/biocontainers/hificnv:1.0.0--h9ee0642_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(maf_vcf), path(expected_cn_bed)
+    tuple val(meta), path(bam), path(bai), path(maf_vcf), val(sex)
     tuple val(meta2), path(fasta)
-    path(exclude_bed)
+    tuple val(meta3), path(expected_xy_bed)
+    tuple val(meta4), path(expected_xx_bed)
+    tuple val(meta5), path(exclude_bed)
 
     output:
     tuple val(meta), path("*.vcf.gz")  , emit: vcf
@@ -26,10 +29,14 @@ process HIFICNV {
     def args    = task.ext.args ?: ''
     prefix      = task.ext.prefix ?: "${meta.id}"
 
-    def expected_cn = expected_cn_bed ? "--expected-cn ${expected_cn_bed}" : ""
+    def expected_cn = (sex == 1 && expected_xy_bed) ? "--expected-cn ${expected_xy_bed}" : (sex == 2 && expected_xx_bed) ? "--expected-cn ${expected_xx_bed}" : ""
     def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
     def maf = maf_vcf ? "--maf ${maf_vcf}" : ""
 
+    if ("$maf_vcf" == "${prefix}.vcf.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    mv_maf = maf ? "mv hificnv.*.maf.bw ${prefix}.maf.bw" : ''
+
     """
     hificnv \\
         $args \\
@@ -38,8 +45,13 @@ process HIFICNV {
         $exclude \\
         $maf \\
         --ref ${fasta} \\
-        --threads ${task.cpus} \\
-        --output-prefix ${prefix}
+        --threads ${task.cpus}
+
+    mv hificnv.*.vcf.gz ${prefix}.vcf.gz
+    mv hificnv.*.depth.bw ${prefix}.depth.bw
+    $mv_maf
+    mv hificnv.*.copynum.bedgraph ${prefix}.copynum.bedgraph
+    mv *.log ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -50,9 +62,12 @@ process HIFICNV {
     stub:
     prefix      = task.ext.prefix ?: "${meta.id}"
 
+    if ("$maf_vcf" == "${prefix}.vcf.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    def maf = maf_vcf ? "touch ${prefix}.maf.bw" : ""
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.depth.bw
+    $maf
     touch ${prefix}.bedgraph
     touch ${prefix}.log
 
diff --git a/modules/local/trgt/main.nf b/modules/local/trgt/main.nf
deleted file mode 100644
index 0c493bf4..00000000
--- a/modules/local/trgt/main.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-process TRGT {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "biocontainers/trgt:0.7.0--hdfd78af_0"
-
-    input:
-    tuple val(meta), path(bam), path(bai), val(sex)
-    tuple val(meta2), path(fasta)
-    tuple val(meta3), path(fai)
-    path(repeats)
-
-    output:
-    tuple val(meta), path("${meta.id}.spanning.bam"), emit: bam
-    tuple val(meta), path("${meta.id}.vcf.gz")      , emit: vcf
-    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}"
-
-    if (sex == 1) {
-        karyotype = "XY"
-    } else if (sex == 2) {
-        karyotype = "XX"
-    }
-
-    """
-    trgt \\
-        $args \\
-        --genome ${fasta} \\
-        --karyotype ${karyotype} \\
-        --repeats ${repeats} \\
-        --reads ${bam} \\
-        --threads ${task.cpus} \\
-        --output-prefix ${meta.id}
-
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        trgt: \$(echo \$(trgt -V) | sed 's/TRGT //' )
-    END_VERSIONS
-    """
-}
-
diff --git a/modules/local/whatshap/haplotag/main.nf b/modules/local/whatshap/haplotag/main.nf
index d4cce45e..9df8d450 100644
--- a/modules/local/whatshap/haplotag/main.nf
+++ b/modules/local/whatshap/haplotag/main.nf
@@ -2,10 +2,10 @@ process WHATSHAP_HAPLOTAG {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::whatshap=2.2"
+    conda "bioconda::whatshap=2.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/whatshap:2.2--py39h1f90b4d_1' :
-        'quay.io/biocontainers/whatshap:2.2--py39h1f90b4d_1' }"
+        'https://depot.galaxyproject.org/singularity/whatshap:2.3--py38h2494328_0' :
+        'quay.io/biocontainers/whatshap:2.3--py38h2494328_0' }"
 
     input:
     tuple val(meta),  path(vcf), path(tbi), path(bam), path(bai)
diff --git a/modules/local/whatshap/phase/main.nf b/modules/local/whatshap/phase/main.nf
index 158046f1..6fd7d674 100644
--- a/modules/local/whatshap/phase/main.nf
+++ b/modules/local/whatshap/phase/main.nf
@@ -2,8 +2,10 @@ process WHATSHAP_PHASE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::whatshap=2.2 bioconda::tabix=1.11"
-    container "docker.io/fellen31/whatshap-tabix:2.2"
+    conda "bioconda::whatshap=2.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/whatshap:2.3--py38h2494328_0' :
+        'quay.io/biocontainers/whatshap:2.3--py38h2494328_0' }"
 
     input:
     tuple val(meta), path(vcf), path(bam), path(bai)
diff --git a/modules/local/whatshap/stats/main.nf b/modules/local/whatshap/stats/main.nf
index 398f3013..c2074328 100644
--- a/modules/local/whatshap/stats/main.nf
+++ b/modules/local/whatshap/stats/main.nf
@@ -2,8 +2,10 @@ process WHATSHAP_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::whatshap=2.2 bioconda::tabix=1.11"
-    container "docker.io/fellen31/whatshap-tabix:2.2"
+    conda "bioconda::whatshap=2.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/whatshap:2.3--py38h2494328_0' :
+        'quay.io/biocontainers/whatshap:2.3--py38h2494328_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
@@ -36,7 +38,7 @@ process WHATSHAP_STATS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.stats.tsv.gz
+    touch ${prefix}.stats.tsv
     touch ${prefix}.blocks.tsv
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff
index 391089ff..8d3f5541 100644
--- a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff
+++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff
@@ -1,33 +1,17 @@
 Changes in module 'nf-core/bcftools/annotate'
---- modules/nf-core/bcftools/annotate/meta.yml
-+++ modules/nf-core/bcftools/annotate/meta.yml
-@@ -34,6 +34,9 @@
-   - header_lines:
-       type: file
-       description: Contains lines to append to the output VCF header
-+  - rename_chrs:
-+      type: file
-+      description: Contains new and old chromosome names
- output:
-   - meta:
-       type: map
-
+'modules/nf-core/bcftools/annotate/meta.yml' is unchanged
+Changes in 'bcftools/annotate/main.nf':
 --- modules/nf-core/bcftools/annotate/main.nf
 +++ modules/nf-core/bcftools/annotate/main.nf
-@@ -8,10 +8,9 @@
-         'biocontainers/bcftools:1.20--h8b25389_0' }"
- 
+@@ -10,6 +10,7 @@
      input:
--    tuple val(meta), path(input), path(index)
--    path(annotations)
--    path(annotations_index)
-+    tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
+     tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
      path(header_lines)
 +    path(rename_chrs)
  
      output:
      tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
-@@ -27,6 +26,7 @@
+@@ -25,6 +26,7 @@
      def prefix  = task.ext.prefix ?: "${meta.id}"
      def header_file = header_lines ? "--header-lines ${header_lines}" : ''
      def annotations_file = annotations ? "--annotations ${annotations}" : ''
@@ -35,13 +19,22 @@ Changes in module 'nf-core/bcftools/annotate'
      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" :
-@@ -43,6 +43,7 @@
+@@ -40,6 +42,7 @@
+         annotate \\
          $args \\
          $annotations_file \\
-         $header_file \\
 +        $rename_chrs_file \\
+         $header_file \\
          --output ${prefix}.${extension} \\
          --threads $task.cpus \\
-         $input
 
+'modules/nf-core/bcftools/annotate/environment.yml' is unchanged
+'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged
+'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged
+'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged
+'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged
+'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged
+'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged
+'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged
 ************************************************************
diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml
index 3d4e3379..5c00b116 100644
--- a/modules/nf-core/bcftools/annotate/environment.yml
+++ b/modules/nf-core/bcftools/annotate/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_annotate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
index 06eb6d34..b6b73309 100644
--- a/modules/nf-core/bcftools/annotate/main.nf
+++ b/modules/nf-core/bcftools/annotate/main.nf
@@ -42,8 +42,8 @@ process BCFTOOLS_ANNOTATE {
         annotate \\
         $args \\
         $annotations_file \\
-        $header_file \\
         $rename_chrs_file \\
+        $header_file \\
         --output ${prefix}.${extension} \\
         --threads $task.cpus \\
         $input
@@ -62,12 +62,12 @@ process BCFTOOLS_ANNOTATE {
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                     "vcf"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
+    def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                        args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                        args.contains("--write-index") || args.contains("-W") ? "csi" :
+                        ""
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+    def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : ""
 
     """
     ${create_cmd} ${prefix}.${extension}
diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml
index 78f806a4..5bfccd2b 100644
--- a/modules/nf-core/bcftools/annotate/meta.yml
+++ b/modules/nf-core/bcftools/annotate/meta.yml
@@ -13,52 +13,64 @@ tools:
       documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: Query VCF or BCF file, can be either uncompressed or compressed
-  - index:
-      type: file
-      description: Index of the query VCF or BCF file
-  - annotations:
-      type: file
-      description: Bgzip-compressed file with annotations
-  - annotations_index:
-      type: file
-      description: Index of the annotations file
-  - header_lines:
-      type: file
-      description: Contains lines to append to the output VCF header
-  - rename_chrs:
-      type: file
-      description: Contains new and old chromosome names
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: Query VCF or BCF file, can be either uncompressed or compressed
+    - index:
+        type: file
+        description: Index of the query VCF or BCF file
+    - annotations:
+        type: file
+        description: Bgzip-compressed file with annotations
+    - annotations_index:
+        type: file
+        description: Index of the annotations file
+  - - header_lines:
+        type: file
+        description: Contains lines to append to the output VCF header
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file
-      description: Compressed annotated VCF file
-      pattern: "*{vcf,vcf.gz,bcf,bcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: Compressed annotated VCF file
+          pattern: "*{vcf,vcf.gz,bcf,bcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@projectoriented"
   - "@ramprasadn"
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test
index 8cd87abc..3a5c4933 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test
@@ -9,20 +9,21 @@ nextflow_process {
     tag "bcftools"
     tag "bcftools/annotate"
 
-    test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") {
 
         config "./vcf.config"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -39,20 +40,21 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") {
 
         config "./vcf.config"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    []]
-
-                input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -68,20 +70,21 @@ nextflow_process {
         }
 
     }
-        test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index") {
+        test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -101,20 +104,21 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -134,20 +138,21 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -166,20 +171,21 @@ nextflow_process {
         }
 
     }
-    test("sarscov2 - [vcf, []], annotation, annotation_tbi, header - bcf_output") {
+    test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") {
 
         config "./bcf.config"
 
         when {
             process {
                 """
-                input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    []])
-
-                input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = Channel.of(
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of(
                     '##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">',
                     '##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">'
                 ).collectFile(name:"headers.vcf", newLine:true)
@@ -199,7 +205,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") {
 
         config "./vcf.config"
         options "-stub"
@@ -207,13 +213,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -227,7 +234,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -235,13 +242,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -256,7 +264,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -264,13 +272,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
@@ -285,7 +294,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub") {
+    test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"
@@ -293,13 +302,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test', 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']['test2_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
-                input[3] = []
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
                 """
             }
         }
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
index 8fd8d11d..bac2224a 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
@@ -1,38 +1,5 @@
 {
-    "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_vcf.vcf.gz.tbi"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-12T16:39:23.802873"
-    },
-    "sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output": {
+    "bcf": {
         "content": [
             [
                 [
@@ -40,7 +7,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test_vcf.vcf.gz"
+                    "test_ann.bcf"
                 ]
             ],
             [
@@ -51,9 +18,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:38:57.039285"
+        "timestamp": "2024-06-12T16:39:33.331888"
     },
-    "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": {
         "content": [
             [
                 [
@@ -84,9 +51,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:39:15.152697"
+        "timestamp": "2024-08-15T10:07:59.658031137"
     },
-    "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": {
         "content": [
             {
                 "0": [
@@ -102,13 +69,25 @@
                     
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "3": [
                     "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
                 ],
                 "csi": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "tbi": [
                     
@@ -131,9 +110,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:39:41.994785"
+        "timestamp": "2024-08-15T10:09:05.096883418"
     },
-    "bcf": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": {
         "content": [
             [
                 [
@@ -141,7 +120,19 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test_ann.bcf"
+                    "test_vcf.vcf.gz"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.csi"
                 ]
             ],
             [
@@ -152,9 +143,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:39:33.331888"
+        "timestamp": "2024-08-15T10:08:10.581301219"
     },
-    "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": {
         "content": [
             {
                 "0": [
@@ -167,13 +158,7 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
                     
@@ -185,13 +170,7 @@
                     
                 ],
                 "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "vcf": [
                     [
@@ -211,9 +190,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:40:13.835994"
+        "timestamp": "2024-08-15T10:08:43.975017625"
     },
-    "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": {
         "content": [
             [
                 [
@@ -223,6 +202,18 @@
                     },
                     "test_vcf.vcf.gz"
                 ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.tbi"
+                ]
+            ],
+            [
+                
             ],
             [
                 "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
@@ -232,9 +223,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:38:48.368629"
+        "timestamp": "2024-08-15T10:08:21.354059092"
     },
-    "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": {
         "content": [
             [
                 [
@@ -246,15 +237,24 @@
                 ]
             ],
             [
-                
-            ],
+                "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T10:07:37.788393317"
+    },
+    "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": {
+        "content": [
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test_vcf.vcf.gz.csi"
+                    "test_vcf.vcf.gz"
                 ]
             ],
             [
@@ -265,9 +265,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:39:05.608108"
+        "timestamp": "2024-08-15T10:07:48.500746325"
     },
-    "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": {
         "content": [
             {
                 "0": [
@@ -280,31 +280,31 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "2": [
+                    
                 ],
                 "3": [
                     "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
                 ],
                 "csi": [
+                    
+                ],
+                "tbi": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "tbi": [
-                    
                 ],
                 "vcf": [
                     [
@@ -324,9 +324,9 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:39:54.842082"
+        "timestamp": "2024-08-15T10:09:16.094918834"
     },
-    "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub": {
+    "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": {
         "content": [
             {
                 "0": [
@@ -383,6 +383,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-12T16:40:04.074052"
+        "timestamp": "2024-08-15T10:08:54.366358502"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml
index 6544e949..5c00b116 100644
--- a/modules/nf-core/bcftools/concat/environment.yml
+++ b/modules/nf-core/bcftools/concat/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_concat
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
index e2337eff..a94b28d8 100644
--- a/modules/nf-core/bcftools/concat/main.nf
+++ b/modules/nf-core/bcftools/concat/main.nf
@@ -11,18 +11,22 @@ process BCFTOOLS_CONCAT {
     tuple val(meta), path(vcfs), path(tbi)
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
-    tuple val(meta), path("*.tbi"), emit: tbi, optional: true
-    tuple val(meta), path("*.csi"), emit: csi, optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("${prefix}.vcf.gz")    , emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true
+    path  "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name }
+    def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n    ")
     """
+    ${create_input_index}
+
     bcftools concat \\
         --output ${prefix}.vcf.gz \\
         $args \\
@@ -37,7 +41,7 @@ process BCFTOOLS_CONCAT {
 
     stub:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
     def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
                 args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
                 args.contains("--write-index") || args.contains("-W") ? "csi" :
diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml
index eeeb2071..d2565b28 100644
--- a/modules/nf-core/bcftools/concat/meta.yml
+++ b/modules/nf-core/bcftools/concat/meta.yml
@@ -13,44 +13,68 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcfs:
-      type: list
-      description: |
-        List containing 2 or more vcf files
-        e.g. [ 'file1.vcf', 'file2.vcf' ]
-  - tbi:
-      type: list
-      description: |
-        List containing 2 or more index files (optional)
-        e.g. [ 'file1.tbi', 'file2.tbi' ]
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcfs:
+        type: list
+        description: |
+          List containing 2 or more vcf files
+          e.g. [ 'file1.vcf', 'file2.vcf' ]
+    - tbi:
+        type: list
+        description: |
+          List containing 2 or more index files (optional)
+          e.g. [ 'file1.tbi', 'file2.tbi' ]
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file
-      description: VCF concatenated output file
-      pattern: "*.{vcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{vcf.gz}"
+      - ${prefix}.vcf.gz:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{vcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.tbi"
+      - ${prefix}.vcf.gz.tbi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.csi"
+      - ${prefix}.vcf.gz.csi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@nvnieuwk"
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test
index cea386e3..cb4642b2 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "bcftools/concat"
 
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") {
 
         config "./nextflow.config"
 
@@ -41,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
@@ -78,7 +78,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
@@ -115,7 +115,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
@@ -153,7 +153,7 @@ nextflow_process {
     }
 
 
-    test("sarscov2 - [[vcf1, vcf2], []]") {
+    test("homo_sapiens - [[vcf1, vcf2], []]") {
 
         config "./nextflow.config"
 
@@ -181,7 +181,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
 
         config "./nextflow.config"
         options "-stub"
@@ -213,7 +213,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -246,7 +246,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -279,7 +279,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
index 1182854f..09e87cd3 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": {
         "content": [
             {
                 "0": [
@@ -49,12 +49,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T08:09:13.734103412"
+        "timestamp": "2024-09-26T11:04:11.178539482"
     },
-    "sarscov2 - [[vcf1, vcf2], []]": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": {
         "content": [
             {
                 "0": [
@@ -94,12 +94,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:09.213249578"
+        "timestamp": "2024-09-26T11:03:08.765639958"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
         "content": [
             [
                 [
@@ -125,12 +125,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T08:08:23.981388325"
+        "timestamp": "2024-09-26T11:03:21.607274757"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
         "content": [
             {
                 "0": [
@@ -142,29 +142,29 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "2": [
+                    
                 ],
                 "3": [
                     "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
                 ],
                 "csi": [
+                    
+                ],
+                "tbi": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "tbi": [
-                    
                 ],
                 "vcf": [
                     [
@@ -180,12 +180,43 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-26T11:04:27.332133878"
+    },
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test3"
+                    },
+                    "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test3"
+                    },
+                    "test3_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:01:24.419027693"
+        "timestamp": "2024-09-26T11:03:36.575719606"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": {
+    "homo_sapiens - [[vcf1, vcf2], []]": {
         "content": [
             {
                 "0": [
@@ -225,43 +256,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:03.597061078"
+        "timestamp": "2024-09-26T11:03:54.069826178"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3_vcf.vcf.gz.csi"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-05T14:00:10.868487669"
-    },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
             {
                 "0": [
@@ -301,12 +301,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:14.836256897"
+        "timestamp": "2024-09-26T11:04:02.45346063"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": {
         "content": [
             [
                 [
@@ -332,12 +332,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:00:31.061411617"
+        "timestamp": "2024-09-26T11:03:44.618596639"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": {
         "content": [
             {
                 "0": [
@@ -349,29 +349,29 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "2": [
-                    
                 ],
                 "3": [
                     "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
                 ],
                 "csi": [
-                    
-                ],
-                "tbi": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "tbi": [
+                    
                 ],
                 "vcf": [
                     [
@@ -387,9 +387,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:01:35.209746508"
+        "timestamp": "2024-09-26T11:04:19.745768656"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
index ea752646..5c00b116 100644
--- a/modules/nf-core/bcftools/index/environment.yml
+++ b/modules/nf-core/bcftools/index/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_index
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/index/meta.yml b/modules/nf-core/bcftools/index/meta.yml
index 0207d057..6897d1bd 100644
--- a/modules/nf-core/bcftools/index/meta.yml
+++ b/modules/nf-core/bcftools/index/meta.yml
@@ -8,40 +8,55 @@ keywords:
   - tbi
 tools:
   - bcftools:
-      description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
+      description: BCFtools is a set of utilities that manipulate variant calls in the
+        Variant Call Format (VCF) and its binary counterpart BCF. All commands work
+        transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most
+        commands accept VCF, bgzipped VCF and BCF with filetype detected automatically
+        even when streaming from a pipe. Indexed VCF and BCF will work in all situations.
+        Un-indexed VCF and BCF and streams will work in most, but not all situations.
       homepage: https://samtools.github.io/bcftools/
       documentation: https://samtools.github.io/bcftools/howtos/index.html
       tool_dev_url: https://github.com/samtools/bcftools
       doi: "10.1093/gigascience/giab008"
       licence: ["MIT", "GPL-3.0-or-later"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: VCF file (optionally GZIPPED)
-      pattern: "*.{vcf,vcf.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF file (optionally GZIPPED)
+        pattern: "*.{vcf,vcf.gz}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
   - csi:
-      type: file
-      description: Default VCF file index file
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index file
+          pattern: "*.csi"
   - tbi:
-      type: file
-      description: Alternative VCF file index file for larger files (activated with -t parameter)
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index file for larger files (activated with
+            -t parameter)
+          pattern: "*.tbi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software version
+          pattern: "versions.yml"
 authors:
   - "@jfy133"
 maintainers:
diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml
deleted file mode 100644
index 87707140..00000000
--- a/modules/nf-core/bcftools/merge/meta.yml
+++ /dev/null
@@ -1,88 +0,0 @@
-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/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml
index 0c7dfa8f..5c00b116 100644
--- a/modules/nf-core/bcftools/norm/environment.yml
+++ b/modules/nf-core/bcftools/norm/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_norm
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf
index 97658267..bd7a2501 100644
--- a/modules/nf-core/bcftools/norm/main.nf
+++ b/modules/nf-core/bcftools/norm/main.nf
@@ -32,7 +32,7 @@ process BCFTOOLS_NORM {
     """
     bcftools norm \\
         --fasta-ref ${fasta} \\
-        --output ${prefix}.${extension}\\
+        --output ${prefix}.${extension} \\
         $args \\
         --threads $task.cpus \\
         ${vcf}
diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml
index a0cdeaf1..b6edeb4a 100644
--- a/modules/nf-core/bcftools/norm/meta.yml
+++ b/modules/nf-core/bcftools/norm/meta.yml
@@ -13,54 +13,70 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: |
-        The vcf file to be normalized
-        e.g. 'file1.vcf'
-      pattern: "*.{vcf,vcf.gz}"
-  - tbi:
-      type: file
-      description: |
-        An optional index of the VCF file (for when the VCF is compressed)
-      pattern: "*.vcf.gz.tbi"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: FASTA reference file
-      pattern: "*.{fasta,fa}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          The vcf file to be normalized
+          e.g. 'file1.vcf'
+        pattern: "*.{vcf,vcf.gz}"
+    - tbi:
+        type: file
+        description: |
+          An optional index of the VCF file (for when the VCF is compressed)
+        pattern: "*.vcf.gz.tbi"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: FASTA reference file
+        pattern: "*.{fasta,fa}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file
-      description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed
+            BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@ramprasadn"
diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml
index 1f7bb1ff..5c00b116 100644
--- a/modules/nf-core/bcftools/pluginsplit/environment.yml
+++ b/modules/nf-core/bcftools/pluginsplit/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_pluginsplit
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml
index 64bfce0a..41f76658 100644
--- a/modules/nf-core/bcftools/pluginsplit/meta.yml
+++ b/modules/nf-core/bcftools/pluginsplit/meta.yml
@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "bcftools_pluginsplit"
 description: Split VCF by sample, creating single- or multi-sample VCFs.
@@ -14,60 +13,83 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: The VCF file to split
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+    - tbi:
+        type: file
+        description: OPTIONAL - The index of the input VCF/BCF
+        pattern: "*.tbi"
+  - - samples:
+        type: file
+        description: |
+          A tab-separated file determining which samples should be in which output file
+          column 1: The sample name(s) in the input file
+          column 2: The sample name(s) to use in the output file (use `-` to keep the original name)
+          column 3: The name of the output file
+          Either this or a groups file should be given
+        pattern: "*"
+  - - groups:
+        type: file
+        description: |
+          A tab-separated file determining which samples should be in which output file(s)
+          column 1: The sample name(s) in the input file
+          column 2: The sample name(s) to use in the output file (use `-` to keep the original name)
+          column 3: The name of the output file(s)
+          Either this or a samples file should be given
+        pattern: "*"
+  - - regions:
+        type: file
+        description: A BED file containing regions to use
+        pattern: "*.bed"
+  - - targets:
+        type: file
+        description: A BED file containing regions to use (but streams rather than index-jumps)
+        pattern: "*.bed"
+output:
   - vcf:
-      type: file
-      description: The VCF file to split
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: The resulting VCF files from the split
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
   - tbi:
-      type: file
-      description: OPTIONAL - The index of the input VCF/BCF
-      pattern: "*.tbi"
-  - samples:
-      type: file
-      description: |
-        A tab-separated file determining which samples should be in which output file
-        column 1: The sample name(s) in the input file
-        column 2: The sample name(s) to use in the output file (use `-` to keep the original name)
-        column 3: The name of the output file
-        Either this or a groups file should be given
-      pattern: "*"
-  - groups:
-      type: file
-      description: |
-        A tab-separated file determining which samples should be in which output file(s)
-        column 1: The sample name(s) in the input file
-        column 2: The sample name(s) to use in the output file (use `-` to keep the original name)
-        column 3: The name of the output file(s)
-        Either this or a samples file should be given
-      pattern: "*"
-  - regions:
-      type: file
-      description: A BED file containing regions to use
-      pattern: "*.bed"
-  - targets:
-      type: file
-      description: A BED file containing regions to use (but streams rather than index-jumps)
-      pattern: "*.bed"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: TBI file
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: CSI file
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - vcf:
-      type: file
-      description: The resulting VCF files from the split
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/local/trgt/enviroment.yml b/modules/nf-core/bcftools/query/environment.yml
similarity index 51%
rename from modules/local/trgt/enviroment.yml
rename to modules/nf-core/bcftools/query/environment.yml
index e6c0944a..5c00b116 100644
--- a/modules/local/trgt/enviroment.yml
+++ b/modules/nf-core/bcftools/query/environment.yml
@@ -1,7 +1,5 @@
-name: trgt
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::trgt=0.4.0
+  - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
new file mode 100644
index 00000000..58019f4d
--- /dev/null
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -0,0 +1,56 @@
+process BCFTOOLS_QUERY {
+    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/bcftools:1.20--h8b25389_0':
+        'biocontainers/bcftools:1.20--h8b25389_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    path regions
+    path targets
+    path samples
+
+    output:
+    tuple val(meta), path("*.${suffix}"), emit: output
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
+    def regions_file = regions ? "--regions-file ${regions}" : ""
+    def targets_file = targets ? "--targets-file ${targets}" : ""
+    def samples_file =  samples ? "--samples-file ${samples}" : ""
+    """
+    bcftools query \\
+        $regions_file \\
+        $targets_file \\
+        $samples_file \\
+        $args \\
+        $vcf \\
+        > ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
+    """
+    touch ${prefix}.${suffix} \\
+
+    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/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml
new file mode 100644
index 00000000..279b3205
--- /dev/null
+++ b/modules/nf-core/bcftools/query/meta.yml
@@ -0,0 +1,67 @@
+name: bcftools_query
+description: Extracts fields from VCF or BCF files and outputs them in user-defined
+  format.
+keywords:
+  - query
+  - variant calling
+  - bcftools
+  - VCF
+tools:
+  - query:
+      description: |
+        Extracts fields from VCF or BCF files and outputs them in user-defined format.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:bcftools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          The vcf file to be qeuried.
+        pattern: "*.{vcf.gz, vcf}"
+    - tbi:
+        type: file
+        description: |
+          The tab index for the VCF file to be inspected.
+        pattern: "*.tbi"
+  - - regions:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file.
+  - - targets:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
+  - - samples:
+        type: file
+        description: |
+          Optional, file of sample names to be included or excluded.
+          e.g. 'file.tsv'
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${suffix}":
+          type: file
+          description: BCFTools query output file
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@drpatelh"
+maintainers:
+  - "@abhi18av"
+  - "@drpatelh"
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test
new file mode 100644
index 00000000..39e67b35
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_QUERY"
+    script "../main.nf"
+    process "BCFTOOLS_QUERY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/query"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - [vcf, tbi], [], [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.output,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], vcf, tsv, []") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.output,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], [], [], [] - stub") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.output[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
new file mode 100644
index 00000000..3ead1f2c
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "sarscov2 - [vcf, tbi], vcf, tsv, []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out"
+                    },
+                    "out.txt:md5,75a6bd0084e2e1838cf7baba11b99d19"
+                ]
+            ],
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:44.916249758"
+    },
+    "sarscov2 - [vcf, tbi], [], [], [] - stub": {
+        "content": [
+            "out.txt",
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:49.932359271"
+    },
+    "sarscov2 - [vcf, tbi], [], [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out"
+                    },
+                    "out.txt:md5,87a2ab194e1ee3219b44e58429ec3307"
+                ]
+            ],
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:39.930697926"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/query/tests/nextflow.config b/modules/nf-core/bcftools/query/tests/nextflow.config
new file mode 100644
index 00000000..da81c2a0
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'"
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/query/tests/tags.yml b/modules/nf-core/bcftools/query/tests/tags.yml
new file mode 100644
index 00000000..fb9455cb
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/query:
+  - "modules/nf-core/bcftools/query/**"
diff --git a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff b/modules/nf-core/bcftools/reheader/bcftools-reheader.diff
deleted file mode 100644
index 65ddb0a2..00000000
--- a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff
+++ /dev/null
@@ -1,28 +0,0 @@
-Changes in module 'nf-core/bcftools/reheader'
---- modules/nf-core/bcftools/reheader/main.nf
-+++ modules/nf-core/bcftools/reheader/main.nf
-@@ -32,17 +32,14 @@
-                     args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
-                     "vcf"
-     """
-+    echo "${meta.id}" > samples
-+    
-     bcftools \\
-         reheader \\
--        $fai_argument \\
--        $header_argument \\
--        $samples_argument \\
--        $args \\
--        --threads $task.cpus \\
-+        -s samples \\
-         $vcf \\
--        | bcftools view \\
--        $args2 \\
--        --output ${prefix}.${extension}
-+        > ${prefix}.reheader.vcf    
-+
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-************************************************************
diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml
index 48fd72c9..5c00b116 100644
--- a/modules/nf-core/bcftools/reheader/environment.yml
+++ b/modules/nf-core/bcftools/reheader/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_reheader
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf
index e1cf0091..9cf6d0d3 100644
--- a/modules/nf-core/bcftools/reheader/main.nf
+++ b/modules/nf-core/bcftools/reheader/main.nf
@@ -13,6 +13,7 @@ process BCFTOOLS_REHEADER {
 
     output:
     tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.{csi,tbi}")              , emit: index, optional: true
     path "versions.yml"                               , emit: versions
 
     when:
@@ -32,14 +33,17 @@ process BCFTOOLS_REHEADER {
                     args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
                     "vcf"
     """
-    echo "${meta.id}" > samples
-    
     bcftools \\
         reheader \\
-        -s samples \\
+        $fai_argument \\
+        $header_argument \\
+        $samples_argument \\
+        $args \\
+        --threads $task.cpus \\
         $vcf \\
-        > ${prefix}.reheader.vcf    
-
+        | bcftools view \\
+        $args2 \\
+        --output ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -56,8 +60,16 @@ process BCFTOOLS_REHEADER {
                     args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" :
                     args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
                     "vcf"
+    def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" :
+                args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" :
+                args2.contains("--write-index") || args2.contains("-W") ? "csi" :
+                ""
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+
     """
-    touch ${prefix}.${extension}
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml
index 690d4ead..47e5344c 100644
--- a/modules/nf-core/bcftools/reheader/meta.yml
+++ b/modules/nf-core/bcftools/reheader/meta.yml
@@ -12,47 +12,60 @@ tools:
       documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
       doi: 10.1093/gigascience/giab008
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: VCF/BCF file
-      pattern: "*.{vcf.gz,vcf,bcf}"
-  - header:
-      type: file
-      description: New header to add to the VCF
-      pattern: "*.{header.txt}"
-  - samples:
-      type: file
-      description: File containing sample names to update (one sample per line)
-      pattern: "*.{samples.txt}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fai:
-      type: file
-      description: Fasta index to update header sequences with
-      pattern: "*.{fai}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF/BCF file
+        pattern: "*.{vcf.gz,vcf,bcf}"
+    - header:
+        type: file
+        description: New header to add to the VCF
+        pattern: "*.{header.txt}"
+    - samples:
+        type: file
+        description: File containing sample names to update (one sample per line)
+        pattern: "*.{samples.txt}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: Fasta index to update header sequences with
+        pattern: "*.{fai}"
 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"
   - vcf:
-      type: file
-      description: VCF with updated header, bgzipped per default
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: VCF with updated header, bgzipped per default
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{csi,tbi}":
+          type: file
+          description: Index of VCF with updated header
+          pattern: "*.{csi,tbi}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@bjohnnyd"
   - "@jemten"
diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test b/modules/nf-core/bcftools/reheader/tests/main.nf.test
index f3200cb3..96c1b7b0 100644
--- a/modules/nf-core/bcftools/reheader/tests/main.nf.test
+++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test
@@ -17,13 +17,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     [],
                     []
                 ]
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -47,13 +47,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     [],
                     []
                 ]
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -68,6 +68,111 @@ nextflow_process {
 
     }
 
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index") {
+
+        config "./vcf_gz_index.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.versions
+                ).match() },
+                { assert process.out.index[0][1].endsWith(".csi") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index") {
+
+        config "./vcf_gz_index_csi.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.versions
+                ).match() },
+                { assert process.out.index[0][1].endsWith(".csi") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index") {
+
+        config "./vcf_gz_index_tbi.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.versions
+                ).match() },
+                { assert process.out.index[0][1].endsWith(".tbi") }
+            )
+        }
+
+    }
+
     test("sarscov2 - [vcf, [], []], fai - bcf output") {
 
         config "./bcf.config"
@@ -77,13 +182,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     [],
                     []
                 ]
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -107,11 +212,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
                     []
                 ]
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
                     []
                 ]
@@ -137,15 +242,15 @@ nextflow_process {
                 """
                 ch_no_samples = Channel.of([
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     []
                 ])
                 ch_samples = Channel.of(["samples.txt", "new_name"])
                     .collectFile(newLine:true)
                 input[0] = ch_no_samples.combine(ch_samples)
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -170,13 +275,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     [],
                     []
                 ]
-                input[1] = [ 
+                input[1] = [
                     [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -193,5 +298,97 @@ nextflow_process {
         }
 
     }
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub") {
+
+        options "-stub"
+        config "./vcf_gz_index.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub") {
+
+        options "-stub"
+        config "./vcf_gz_index_csi.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub") {
+
+        options "-stub"
+        config "./vcf_gz_index_tbi.config"
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 
 }
diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
index 3629393b..87a3654a 100644
--- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap
@@ -1,4 +1,140 @@
 {
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T10:09:05.955833763"
+    },
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T09:52:41.444952182"
+    },
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T09:53:04.314827944"
+    },
     "sarscov2 - [vcf, [], []], fai - vcf output": {
         "content": [
             {
@@ -12,7 +148,13 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    
                 ],
                 "vcf": [
                     [
@@ -32,7 +174,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:52:56.985565049"
+        "timestamp": "2024-09-03T09:50:41.983008108"
     },
     "sarscov2 - [vcf, [], []], fai - bcf output": {
         "content": [
@@ -47,7 +189,13 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    
                 ],
                 "vcf": [
                     [
@@ -67,7 +215,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:53:29.509254578"
+        "timestamp": "2024-09-03T09:51:43.072513252"
     },
     "sarscov2 - [vcf, [], []], fai - vcf.gz output": {
         "content": [
@@ -82,7 +230,13 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    
                 ],
                 "vcf": [
                     [
@@ -102,7 +256,90 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:53:11.468640381"
+        "timestamp": "2024-09-03T09:50:53.055630152"
+    },
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T10:08:37.999924355"
+    },
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T09:52:52.512269206"
     },
     "sarscov2 - [vcf, [], []], fai - stub": {
         "content": [
@@ -117,6 +354,36 @@
         },
         "timestamp": "2024-05-31T15:16:36.337112514"
     },
+    "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-03T10:08:55.434831174"
+    },
     "sarscov2 - [vcf, [], samples], fai": {
         "content": [
             {
@@ -130,7 +397,13 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    
                 ],
                 "vcf": [
                     [
@@ -150,7 +423,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:54:04.84196388"
+        "timestamp": "2024-09-03T09:52:12.216002665"
     },
     "sarscov2 - [vcf, header, []], []": {
         "content": [
@@ -165,7 +438,13 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34"
+                ],
+                "index": [
+                    
                 ],
                 "vcf": [
                     [
@@ -185,6 +464,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-03T11:53:44.311122728"
+        "timestamp": "2024-09-03T09:51:54.062386022"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config
new file mode 100644
index 00000000..1e050ec7
--- /dev/null
+++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config
@@ -0,0 +1,4 @@
+process {
+    ext.prefix = { "${meta.id}_vcf" }
+    ext.args2 = "--output-type z --write-index --no-version"
+}
diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config
new file mode 100644
index 00000000..536e4b42
--- /dev/null
+++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config
@@ -0,0 +1,4 @@
+process {
+    ext.prefix = { "${meta.id}_vcf" }
+    ext.args2 = "--output-type z --write-index=csi --no-version"
+}
diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config
new file mode 100644
index 00000000..91a80db7
--- /dev/null
+++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config
@@ -0,0 +1,5 @@
+process {
+    ext.prefix = { "${meta.id}_vcf" }
+    ext.args2 = "--output-type z --write-index=tbi --no-version"
+
+}
diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml
index 2295ecfd..5c00b116 100644
--- a/modules/nf-core/bcftools/sort/environment.yml
+++ b/modules/nf-core/bcftools/sort/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_sort
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml
index dfbddcba..f7a6eff1 100644
--- a/modules/nf-core/bcftools/sort/meta.yml
+++ b/modules/nf-core/bcftools/sort/meta.yml
@@ -12,38 +12,53 @@ tools:
       tool_dev_url: https://github.com/samtools/bcftools
       doi: "10.1093/bioinformatics/btp352"
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: The VCF/BCF file to be sorted
-      pattern: "*.{vcf.gz,vcf,bcf}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: The VCF/BCF file to be sorted
+        pattern: "*.{vcf.gz,vcf,bcf}"
 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"
   - vcf:
-      type: file
-      description: Sorted VCF file
-      pattern: "*.{vcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: Sorted VCF file
+          pattern: "*.{vcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@Gwennid"
 maintainers:
diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml
index 128fe204..93357b41 100644
--- a/modules/nf-core/bcftools/stats/environment.yml
+++ b/modules/nf-core/bcftools/stats/environment.yml
@@ -1,8 +1,6 @@
-name: bcftools_stats
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
   - bioconda::htslib=1.20
diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml
index 7ea2103e..655a61c5 100644
--- a/modules/nf-core/bcftools/stats/meta.yml
+++ b/modules/nf-core/bcftools/stats/meta.yml
@@ -13,58 +13,86 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: VCF input file
-      pattern: "*.{vcf}"
-  - tbi:
-      type: file
-      description: |
-        The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
-      pattern: "*.tbi"
-  - regions:
-      type: file
-      description: |
-        Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
-  - targets:
-      type: file
-      description: |
-        Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)
-  - samples:
-      type: file
-      description: |
-        Optional, file of sample names to be included or excluded.
-        e.g. 'file.tsv'
-  - exons:
-      type: file
-      description: |
-        Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).
-        e.g. 'exons.tsv.gz'
-  - fasta:
-      type: file
-      description: |
-        Faidx indexed reference sequence file to determine INDEL context.
-        e.g. 'reference.fa'
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF input file
+        pattern: "*.{vcf}"
+    - tbi:
+        type: file
+        description: |
+          The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
+        pattern: "*.tbi"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - regions:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - targets:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - samples:
+        type: file
+        description: |
+          Optional, file of sample names to be included or excluded.
+          e.g. 'file.tsv'
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - exons:
+        type: file
+        description: |
+          Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).
+          e.g. 'exons.tsv.gz'
+  - - meta6:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: |
+          Faidx indexed reference sequence file to determine INDEL context.
+          e.g. 'reference.fa'
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - stats:
-      type: file
-      description: Text output file containing stats
-      pattern: "*_{stats.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*stats.txt":
+          type: file
+          description: Text output file containing stats
+          pattern: "*_{stats.txt}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml
index 4b2a21df..5c00b116 100644
--- a/modules/nf-core/bcftools/view/environment.yml
+++ b/modules/nf-core/bcftools/view/environment.yml
@@ -1,7 +1,5 @@
-name: bcftools_view
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml
index 5eb1b196..aa7785f1 100644
--- a/modules/nf-core/bcftools/view/meta.yml
+++ b/modules/nf-core/bcftools/view/meta.yml
@@ -1,5 +1,6 @@
 name: bcftools_view
-description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
+description: View, subset and filter VCF or BCF files by position and filtering expression.
+  Convert between VCF and BCF
 keywords:
   - variant calling
   - view
@@ -13,59 +14,74 @@ tools:
       documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: |
-        The vcf file to be inspected.
-        e.g. 'file.vcf'
-  - index:
-      type: file
-      description: |
-        The tab index for the VCF file to be inspected.
-        e.g. 'file.tbi'
-  - regions:
-      type: file
-      description: |
-        Optionally, restrict the operation to regions listed in this file.
-        e.g. 'file.vcf'
-  - targets:
-      type: file
-      description: |
-        Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
-        e.g. 'file.vcf'
-  - samples:
-      type: file
-      description: |
-        Optional, file of sample names to be included or excluded.
-        e.g. 'file.tsv'
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          The vcf file to be inspected.
+          e.g. 'file.vcf'
+    - index:
+        type: file
+        description: |
+          The tab index for the VCF file to be inspected.
+          e.g. 'file.tbi'
+  - - regions:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file.
+          e.g. 'file.vcf'
+  - - targets:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
+          e.g. 'file.vcf'
+  - - samples:
+        type: file
+        description: |
+          Optional, file of sample names to be included or excluded.
+          e.g. 'file.tsv'
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file
-      description: VCF normalized output file
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: VCF normalized output file
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
 maintainers:
diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml
index 99707878..5683bc05 100644
--- a/modules/nf-core/bedtools/merge/environment.yml
+++ b/modules/nf-core/bedtools/merge/environment.yml
@@ -1,7 +1,5 @@
-name: bedtools_merge
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bedtools=2.31.1
diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml
index d7463e3d..6da54205 100644
--- a/modules/nf-core/bedtools/merge/meta.yml
+++ b/modules/nf-core/bedtools/merge/meta.yml
@@ -1,5 +1,6 @@
 name: bedtools_merge
-description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
+description: combines overlapping or “book-ended” features in an interval file into
+  a single feature which spans all of the combined features.
 keywords:
   - bed
   - merge
@@ -11,30 +12,33 @@ tools:
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
       licence: ["MIT"]
+      identifier: biotools:bedtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bed:
-      type: file
-      description: Input BED file
-      pattern: "*.{bed}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Input BED file
+        pattern: "*.{bed}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bed:
-      type: file
-      description: Overlapped bed file with combined features
-      pattern: "*.{bed}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bed":
+          type: file
+          description: Overlapped bed file with combined features
+          pattern: "*.{bed}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@edmundmiller"
   - "@sruthipsuresh"
diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test
index 95dba8e5..2959d6b9 100644
--- a/modules/nf-core/bedtools/merge/tests/main.nf.test
+++ b/modules/nf-core/bedtools/merge/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test'],
-                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml
index 87b2e425..5683bc05 100644
--- a/modules/nf-core/bedtools/sort/environment.yml
+++ b/modules/nf-core/bedtools/sort/environment.yml
@@ -1,7 +1,5 @@
-name: bedtools_sort
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bedtools=2.31.1
diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml
index 7c915f5f..313698f1 100644
--- a/modules/nf-core/bedtools/sort/meta.yml
+++ b/modules/nf-core/bedtools/sort/meta.yml
@@ -11,35 +11,38 @@ tools:
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
       documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
       licence: ["MIT"]
+      identifier: biotools:bedtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - intervals:
-      type: file
-      description: BED/BEDGRAPH
-      pattern: "*.{bed|bedGraph}"
-  - genome_file:
-      type: file
-      description: |
-        Optional reference genome 2 column file that defines the expected chromosome order.
-      pattern: "*.{fai,txt,chromsizes}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - intervals:
+        type: file
+        description: BED/BEDGRAPH
+        pattern: "*.{bed|bedGraph}"
+  - - genome_file:
+        type: file
+        description: |
+          Optional reference genome 2 column file that defines the expected chromosome order.
+        pattern: "*.{fai,txt,chromsizes}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - sorted:
-      type: file
-      description: Sorted output file
-      pattern: "*.${extension}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${extension}":
+          type: file
+          description: Sorted output file
+          pattern: "*.${extension}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@edmundmiller"
   - "@sruthipsuresh"
diff --git a/modules/nf-core/cadd/cadd.diff b/modules/nf-core/cadd/cadd.diff
index 2ee51723..2243f02d 100644
--- a/modules/nf-core/cadd/cadd.diff
+++ b/modules/nf-core/cadd/cadd.diff
@@ -1,4 +1,6 @@
 Changes in module 'nf-core/cadd'
+'modules/nf-core/cadd/meta.yml' is unchanged
+Changes in 'cadd/main.nf':
 --- modules/nf-core/cadd/main.nf
 +++ modules/nf-core/cadd/main.nf
 @@ -7,13 +7,14 @@
@@ -13,10 +15,12 @@ Changes in module 'nf-core/cadd'
  
      input:
      tuple val(meta), path(vcf)
-     path(annotation_dir)
-+    path(prescored_dir)
+-    path(annotation_dir)
++    tuple val(meta2), path(annotation_dir)
++    tuple val(meta3), path(prescored_dir)
  
      output:
      tuple val(meta), path("*.tsv.gz"), emit: tsv
 
+'modules/nf-core/cadd/environment.yml' is unchanged
 ************************************************************
diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml
index 26f170e9..4477e16e 100644
--- a/modules/nf-core/cadd/environment.yml
+++ b/modules/nf-core/cadd/environment.yml
@@ -1,8 +1,6 @@
-name: cadd
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::cadd-scripts=1.6.post1
   - conda-forge::conda=4.14.0
diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf
index 52490c64..d830ff72 100644
--- a/modules/nf-core/cadd/main.nf
+++ b/modules/nf-core/cadd/main.nf
@@ -13,8 +13,8 @@ process CADD {
 
     input:
     tuple val(meta), path(vcf)
-    path(annotation_dir)
-    path(prescored_dir)
+    tuple val(meta2), path(annotation_dir)
+    tuple val(meta3), path(prescored_dir)
 
     output:
     tuple val(meta), path("*.tsv.gz"), emit: tsv
diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml
index 230ed9c0..751bea45 100644
--- a/modules/nf-core/cadd/meta.yml
+++ b/modules/nf-core/cadd/meta.yml
@@ -1,5 +1,6 @@
 name: "cadd"
-description: CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.
+description: CADD is a tool for scoring the deleteriousness of single nucleotide variants
+  as well as insertion/deletions variants in the human genome.
 keywords:
   - cadd
   - annotate
@@ -13,36 +14,39 @@ tools:
       doi: "10.1093/nar/gky1016"
       licence:
         - Restricted. Free for non-commercial users.
+      identifier: biotools:cadd_phred
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: Input file for annotation in vcf or vcf.gz format
-      pattern: "*.{vcf,vcf.gz}"
-  - annotation_dir:
-      type: file
-      description: |
-        Path to folder containing the vcf files with precomputed CADD scores.
-        This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
-      pattern: "*.{vcf,vcf.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: Input file for annotation in vcf or vcf.gz format
+        pattern: "*.{vcf,vcf.gz}"
+  - - annotation_dir:
+        type: file
+        description: |
+          Path to folder containing the vcf files with precomputed CADD scores.
+          This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
+        pattern: "*.{vcf,vcf.gz}"
 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"
   - tsv:
-      type: file
-      description: Annotated tsv file
-      pattern: "*.{tsv,tsv.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tsv.gz":
+          type: file
+          description: Annotated tsv file
+          pattern: "*.{tsv,tsv.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
index 8c69b121..71e04c3d 100644
--- a/modules/nf-core/cat/fastq/environment.yml
+++ b/modules/nf-core/cat/fastq/environment.yml
@@ -1,7 +1,5 @@
-name: cat_fastq
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - conda-forge::coreutils=8.30
+  - conda-forge::coreutils=9.5
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index b68e5f91..4364a389 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -4,8 +4,8 @@ process CAT_FASTQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' :
+        'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
index db4ac3c7..91ff2fb5 100644
--- a/modules/nf-core/cat/fastq/meta.yml
+++ b/modules/nf-core/cat/fastq/meta.yml
@@ -10,30 +10,33 @@ tools:
         The cat utility reads files sequentially, writing them to the standard output.
       documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files to be concatenated.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files to be concatenated.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - reads:
-      type: file
-      description: Merged fastq file
-      pattern: "*.{merged.fastq.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.merged.fastq.gz":
+          type: file
+          description: Merged fastq file
+          pattern: "*.{merged.fastq.gz}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
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 aec119a9..f8689a1c 100644
--- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:30:39.816981"
+        "timestamp": "2024-10-19T20:02:07.519211144"
     },
     "test_cat_fastq_single_end_same_name": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:32:35.229332"
+        "timestamp": "2024-10-19T20:02:31.618628921"
     },
     "test_cat_fastq_single_end_single_file": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -94,15 +94,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:34:00.058829"
+        "timestamp": "2024-10-19T20:02:57.904149581"
     },
     "test_cat_fastq_paired_end_same_name": {
         "content": [
@@ -120,7 +120,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -135,15 +135,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:33:33.031555"
+        "timestamp": "2024-10-19T20:02:44.577183829"
     },
     "test_cat_fastq_single_end - stub": {
         "content": [
@@ -158,7 +158,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -170,15 +170,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:28.244999"
+        "timestamp": "2024-10-19T20:03:10.603734777"
     },
     "test_cat_fastq_paired_end_same_name - stub": {
         "content": [
@@ -196,7 +196,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -211,15 +211,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:57.070911"
+        "timestamp": "2024-10-19T20:03:46.041808828"
     },
     "test_cat_fastq_single_end_same_name - stub": {
         "content": [
@@ -234,7 +234,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -246,15 +246,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:46.796254"
+        "timestamp": "2024-10-19T20:03:34.13865402"
     },
     "test_cat_fastq_paired_end": {
         "content": [
@@ -272,7 +272,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -287,15 +287,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-01-17T17:32:02.270935"
+        "timestamp": "2024-10-19T20:02:19.64383573"
     },
     "test_cat_fastq_paired_end - stub": {
         "content": [
@@ -313,7 +313,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -328,15 +328,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:07:37.807553"
+        "timestamp": "2024-10-19T20:03:22.597246066"
     },
     "test_cat_fastq_single_end_single_file - stub": {
         "content": [
@@ -351,7 +351,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ],
                 "reads": [
                     [
@@ -363,14 +363,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d42d6e24d67004608495883e00bd501b"
+                    "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:14:51.861264"
+        "timestamp": "2024-10-19T20:03:58.44849001"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/deepvariant/README.md b/modules/nf-core/deepvariant/README.md
deleted file mode 100644
index 9d1ceb34..00000000
--- a/modules/nf-core/deepvariant/README.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# Conda is not supported at the moment
-
-The [bioconda](https://bioconda.github.io/recipes/deepvariant/README.html) recipe is not fully working as expected.
-
-See https://github.com/bioconda/bioconda-recipes/issues/30310 and https://github.com/nf-core/modules/issues/1754 for more information.
-
-Hence, we are using the docker container provided by the authors of the tool:
-
-- [google/deepvariant](https://hub.docker.com/r/google/deepvariant)
-
-This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/deepvariant) for convenience.
diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml
deleted file mode 100644
index 2327dd5f..00000000
--- a/modules/nf-core/deepvariant/meta.yml
+++ /dev/null
@@ -1,92 +0,0 @@
-name: deepvariant
-description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
-keywords:
-  - variant calling
-  - machine learning
-  - neural network
-tools:
-  - deepvariant:
-      description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
-      homepage: https://github.com/google/deepvariant
-      documentation: https://github.com/google/deepvariant
-      tool_dev_url: https://github.com/google/deepvariant
-      doi: "10.1038/nbt.4235"
-      licence: ["BSD-3-clause"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM file
-      pattern: "*.bam/cram"
-  - index:
-      type: file
-      description: Index of BAM/CRAM file
-      pattern: "*.bai/crai"
-  - interval:
-      type: file
-      description: Interval file for targeted regions
-      pattern: "*.bed"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: The reference fasta file
-      pattern: "*.fasta"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fai:
-      type: file
-      description: Index of reference fasta file
-      pattern: "*.fai"
-  - meta4:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - gzi:
-      type: file
-      description: GZI index of reference fasta file
-      pattern: "*.gzi"
-  - meta5:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - par_bed:
-      type: file
-      description: BED file containing PAR regions
-      pattern: "*.bed"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: Compressed VCF file
-      pattern: "*.vcf.gz"
-  - gvcf:
-      type: file
-      description: Compressed GVCF file
-      pattern: "*.g.vcf.gz"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-authors:
-  - "@abhi18av"
-  - "@ramprasadn"
-maintainers:
-  - "@abhi18av"
-  - "@ramprasadn"
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf
similarity index 98%
rename from modules/nf-core/deepvariant/main.nf
rename to modules/nf-core/deepvariant/rundeepvariant/main.nf
index 8d3d0911..7f99c53f 100644
--- a/modules/nf-core/deepvariant/main.nf
+++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf
@@ -1,4 +1,4 @@
-process DEEPVARIANT {
+process DEEPVARIANT_RUNDEEPVARIANT {
     tag "$meta.id"
     label 'process_high'
 
diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml
new file mode 100644
index 00000000..29b45ff9
--- /dev/null
+++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml
@@ -0,0 +1,122 @@
+name: deepvariant_rundeepvariant
+description: DeepVariant is an analysis pipeline that uses a deep neural network to
+  call genetic variants from next-generation DNA sequencing data
+keywords:
+  - variant calling
+  - machine learning
+  - neural network
+tools:
+  - deepvariant:
+      description: DeepVariant is an analysis pipeline that uses a deep neural network
+        to call genetic variants from next-generation DNA sequencing data
+      homepage: https://github.com/google/deepvariant
+      documentation: https://github.com/google/deepvariant
+      tool_dev_url: https://github.com/google/deepvariant
+      doi: "10.1038/nbt.4235"
+      licence: ["BSD-3-clause"]
+      identifier: biotools:deepvariant
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.bam/cram"
+    - index:
+        type: file
+        description: Index of BAM/CRAM file
+        pattern: "*.bai/crai"
+    - intervals:
+        type: file
+        description: file containing intervals
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: Index of reference fasta file
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - gzi:
+        type: file
+        description: GZI index of reference fasta file
+        pattern: "*.gzi"
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - par_bed:
+        type: file
+        description: BED file containing PAR regions
+        pattern: "*.bed"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.vcf.gz:
+          type: file
+          description: Compressed VCF file
+          pattern: "*.vcf.gz"
+  - vcf_tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.vcf.gz.tbi:
+          type: file
+          description: Tabix index file of compressed VCF
+          pattern: "*.vcf.gz.tbi"
+  - gvcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.g.vcf.gz:
+          type: file
+          description: Compressed GVCF file
+          pattern: "*.g.vcf.gz"
+  - gvcf_tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.g.vcf.gz.tbi:
+          type: file
+          description: Tabix index file of compressed GVCF
+          pattern: "*.g.vcf.gz.tbi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@ramprasadn"
+maintainers:
+  - "@abhi18av"
+  - "@ramprasadn"
diff --git a/modules/nf-core/deepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test
similarity index 97%
rename from modules/nf-core/deepvariant/tests/main.nf.test
rename to modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test
index 17765233..0790fb81 100644
--- a/modules/nf-core/deepvariant/tests/main.nf.test
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test
@@ -1,9 +1,10 @@
 nextflow_process {
 
-    name "Test Process DEEPVARIANT"
+    name "Test Process DEEPVARIANT_RUNDEEPVARIANT"
     script "../main.nf"
-    process "DEEPVARIANT"
+    process "DEEPVARIANT_RUNDEEPVARIANT"
 
+    tag "deepvariant/rundeepvariant"
     tag "deepvariant"
     tag "modules"
     tag "modules_nfcore"
@@ -162,4 +163,4 @@ nextflow_process {
         }
     }
 
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/deepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
similarity index 91%
rename from modules/nf-core/deepvariant/tests/main.nf.test.snap
rename to modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
index 04f87774..1ec351ee 100644
--- a/modules/nf-core/deepvariant/tests/main.nf.test.snap
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
@@ -39,7 +39,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ],
                 "gvcf": [
                     [
@@ -78,15 +78,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-01T12:09:40.987117305"
+        "timestamp": "2024-08-29T11:36:27.325363"
     },
     "homo_sapiens - [bam, bai] - fasta - fai": {
         "content": [
@@ -128,7 +128,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ],
                 "gvcf": [
                     [
@@ -167,15 +167,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-01T12:08:47.058887374"
+        "timestamp": "2024-08-29T11:34:41.779153"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": {
         "content": [
@@ -217,7 +217,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ],
                 "gvcf": [
                     [
@@ -256,15 +256,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-01T12:09:13.952808655"
+        "timestamp": "2024-08-29T11:35:16.993129"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": {
         "content": [
@@ -306,7 +306,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ],
                 "gvcf": [
                     [
@@ -345,14 +345,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8"
+                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-23T14:29:24.939680679"
+        "timestamp": "2024-08-29T11:35:52.23093"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/deepvariant/tests/nextflow-intervals.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config
similarity index 70%
rename from modules/nf-core/deepvariant/tests/nextflow-intervals.config
rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config
index 6d135f9f..78d8d598 100644
--- a/modules/nf-core/deepvariant/tests/nextflow-intervals.config
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config
@@ -1,6 +1,6 @@
 process {
 
-    withName: DEEPVARIANT {
+    withName: DEEPVARIANT_RUNDEEPVARIANT {
          ext.args = '--model_type=WGS '
          ext.prefix = { "${meta.id}_out" }
      }
diff --git a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config
similarity index 74%
rename from modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config
rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config
index 4be8986b..6d265292 100644
--- a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config
@@ -1,6 +1,6 @@
 process {
 
-    withName: DEEPVARIANT {
+    withName: DEEPVARIANT_RUNDEEPVARIANT {
          ext.args = '--model_type=WGS --haploid_contigs chr22'
          ext.prefix = { "${meta.id}_out" }
      }
diff --git a/modules/nf-core/deepvariant/tests/nextflow.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config
similarity index 75%
rename from modules/nf-core/deepvariant/tests/nextflow.config
rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config
index d335d30b..77e355ca 100644
--- a/modules/nf-core/deepvariant/tests/nextflow.config
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
 
-    withName: DEEPVARIANT {
+    withName: DEEPVARIANT_RUNDEEPVARIANT {
          ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS '
          ext.prefix = { "${meta.id}_out" }
      }
diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml
new file mode 100644
index 00000000..958b8e41
--- /dev/null
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml
@@ -0,0 +1,2 @@
+deepvariant/rundeepvariant:
+  - modules/nf-core/deepvariant/rundeepvariant/**
diff --git a/modules/nf-core/deepvariant/tests/tags.yml b/modules/nf-core/deepvariant/tests/tags.yml
deleted file mode 100644
index 8e838c7b..00000000
--- a/modules/nf-core/deepvariant/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-deepvariant:
-  - modules/nf-core/deepvariant/**
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/main.nf b/modules/nf-core/deepvariant/vcfstatsreport/main.nf
new file mode 100644
index 00000000..5bbf06b6
--- /dev/null
+++ b/modules/nf-core/deepvariant/vcfstatsreport/main.nf
@@ -0,0 +1,59 @@
+process DEEPVARIANT_VCFSTATSREPORT {
+    tag "$meta.id"
+    label 'process_single'
+
+    // FIXME Conda is not supported at the moment
+    // BUG https://github.com/nf-core/modules/issues/1754
+    // BUG https://github.com/bioconda/bioconda-recipes/issues/30310
+    container "nf-core/deepvariant:1.6.1"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("${prefix}.visual_report.html"), emit: report
+    path "versions.yml"                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
+    // FIXME Revert this on next version bump
+    def VERSION = '1.6.1'
+
+    """
+    /opt/deepvariant/bin/vcf_stats_report \\
+        --input_vcf=${vcf} \\
+        --outfile_base ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepvariant: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    prefix = task.ext.prefix ?: "${meta.id}"
+    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
+    // FIXME Revert this on next version bump
+    def VERSION = '1.6.1'
+    """
+    touch ${prefix}.visual_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepvariant: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/meta.yml b/modules/nf-core/deepvariant/vcfstatsreport/meta.yml
new file mode 100644
index 00000000..c882a1b1
--- /dev/null
+++ b/modules/nf-core/deepvariant/vcfstatsreport/meta.yml
@@ -0,0 +1,47 @@
+name: deepvariant_vcfstatsreport
+description: DeepVariant is an analysis pipeline that uses a deep neural network to
+  call genetic variants from next-generation DNA sequencing data
+keywords:
+  - variant calling
+  - machine learning
+  - neural network
+tools:
+  - deepvariant:
+      description: DeepVariant is an analysis pipeline that uses a deep neural network
+        to call genetic variants from next-generation DNA sequencing data
+      homepage: https://github.com/google/deepvariant
+      documentation: https://github.com/google/deepvariant
+      tool_dev_url: https://github.com/google/deepvariant
+      doi: "10.1038/nbt.4235"
+      licence: ["BSD-3-clause"]
+      identifier: biotools:deepvariant
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF file
+        pattern: "{*.vcf,vcf.gz,bcf,bcf.gz}"
+output:
+  - report:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.visual_report.html:
+          type: file
+          description: Visual report in HTML format
+          pattern: "*.html"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test
new file mode 100644
index 00000000..bec946ef
--- /dev/null
+++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test
@@ -0,0 +1,183 @@
+nextflow_process {
+
+    name "Test Process DEEPVARIANT_VCFSTATSREPORT"
+    script "../main.nf"
+    process "DEEPVARIANT_VCFSTATSREPORT"
+
+    tag "deepvariant/vcfstatsreport"
+    tag "deepvariant"
+    tag "modules"
+    tag "modules_nfcore"
+
+    test("vcf") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("vcf.gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bcf") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bcf.gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("vcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                      file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap
new file mode 100644
index 00000000..9a9ac3ce
--- /dev/null
+++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap
@@ -0,0 +1,266 @@
+{
+    "bcf.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-14T08:19:35.672028563"
+    },
+    "bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-11T07:47:10.485269156"
+    },
+    "vcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-14T08:34:50.411910578"
+    },
+    "vcf.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-11T07:47:00.438649988"
+    },
+    "vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-11T07:44:07.427456921"
+    },
+    "bcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-14T08:35:03.341417618"
+    },
+    "bcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-14T08:35:13.52398762"
+    },
+    "vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-14T08:34:35.977457571"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml b/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml
new file mode 100644
index 00000000..3b1f5922
--- /dev/null
+++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml
@@ -0,0 +1,2 @@
+deepvariant/vcfstatsreport:
+  - modules/nf-core/deepvariant/vcfstatsreport/**
diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
new file mode 100644
index 00000000..3d36eb17
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::ensembl-vep=113.0
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
new file mode 100644
index 00000000..69245df0
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/main.nf
@@ -0,0 +1,49 @@
+process ENSEMBLVEP_FILTERVEP {
+    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/ensembl-vep:113.0--pl5321h2a3209d_0' :
+        'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
+
+    input:
+    tuple val(meta), path(input)
+    path (feature_file)
+
+    output:
+    tuple val(meta), path("*.${extension}"), emit: output
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    extension  = task.ext.suffix ?: "vcf"
+    """
+    filter_vep \\
+        $args \\
+        --input_file $input \\
+        --output_file ${prefix}.${extension} \\
+        --only_matched
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    extension  = task.ext.suffix ?: "vcf"
+    """
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml
new file mode 100644
index 00000000..a73e3b7a
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/meta.yml
@@ -0,0 +1,50 @@
+name: ensemblvep_filtervep
+description: Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
+keywords:
+  - annotation
+  - vcf
+  - tab
+  - filter
+tools:
+  - ensemblvep:
+      description: |
+        VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
+        or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
+      homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
+      documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
+      licence: ["Apache-2.0"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - input:
+        type: file
+        description: VCF/TAB file annotated with vep
+        pattern: "*.{vcf,tab,tsv,txt}"
+  - - feature_file:
+        type: file
+        description: File containing features on separate lines. To be used with --filter
+          option.
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.${extension}":
+          type: file
+          description: VCF/TAB file
+          pattern: "*.{vcf,tab,txt,tsv}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@ramprasadn"
+maintainers:
+  - "@ramprasadn"
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
new file mode 100644
index 00000000..7147792f
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test
@@ -0,0 +1,136 @@
+nextflow_process {
+
+    name "Test Process ENSEMBLVEP_FILTERVEP"
+    script "../main.nf"
+    process "ENSEMBLVEP_FILTERVEP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ensemblvep"
+    tag "ensemblvep/vep"
+    tag "ensemblvep/filtervep"
+    tag "ensemblvep/download"
+
+    // Test for filtering VCF file
+    test("test_ensemblvep_filtervep_vcf") {
+        config "./vcf.config"
+
+        setup {
+            run("ENSEMBLVEP_DOWNLOAD") {
+                script "../../download/main.nf"
+
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id:"113_WBcel235"],
+                        params.vep_genome,
+                        params.vep_species,
+                        params.vep_cache_version
+                    ])
+                    """
+                }
+            }
+            run("ENSEMBLVEP_VEP") {
+                script "../../vep/main.nf"
+
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/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.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ])
+                    input[6] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = ENSEMBLVEP_VEP.out.vcf
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.output.get(0).get(1)).readLines().first().contains("##fileformat=VCFv4.2") }
+            )
+        }
+    }
+
+    // Test for filtering TAB file
+    test("test_ensemblvep_filtervep_tab_gz") {
+        config "./tab.gz.config"
+
+        setup {
+            run("ENSEMBLVEP_DOWNLOAD") {
+                script "../../download/main.nf"
+
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [id:"113_WBcel235"],
+                        params.vep_genome,
+                        params.vep_species,
+                        params.vep_cache_version
+                    ])
+                    """
+                }
+            }
+            run("ENSEMBLVEP_VEP") {
+                script "../../vep/main.nf"
+
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/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.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ])
+                    input[6] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = ENSEMBLVEP_VEP.out.tab
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
new file mode 100644
index 00000000..065d747b
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "test_ensemblvep_filtervep_vcf": {
+        "content": [
+            [
+                "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-21T09:10:47.874831491"
+    },
+    "test_ensemblvep_filtervep_tab_gz": {
+        "content": [
+            [
+                "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-21T09:11:18.765461163"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config
new file mode 100644
index 00000000..40b3a3bd
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config
@@ -0,0 +1,10 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+params {
+    vep_cache_version = "113"
+    vep_genome        = "WBcel235"
+    vep_species       = "caenorhabditis_elegans"
+}
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config
new file mode 100644
index 00000000..cdad2d94
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config
@@ -0,0 +1,24 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: ENSEMBLVEP_DOWNLOAD {
+        ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+    }
+
+    withName: ENSEMBLVEP_VEP {
+        ext.args   = '--tab'
+        ext.prefix = { "${meta.id}_vep" }
+    }
+
+    withName: ENSEMBLVEP_FILTERVEP {
+        ext.args   = '--filter "Feature_type is Transcript"'
+        ext.suffix = "tab"
+    }
+}
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml
new file mode 100644
index 00000000..b43bf40d
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml
@@ -0,0 +1,2 @@
+ensemblvep/filtervep:
+  - "modules/nf-core/ensemblvep/filtervep/**"
diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config
new file mode 100644
index 00000000..ee2aef57
--- /dev/null
+++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config
@@ -0,0 +1,23 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: ENSEMBLVEP_DOWNLOAD {
+        ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+    }
+
+    withName: ENSEMBLVEP_VEP {
+        ext.args   = '--vcf'
+        ext.prefix = { "${meta.id}_vep" }
+    }
+
+    withName: ENSEMBLVEP_FILTERVEP {
+        ext.args = '--filter "Feature_type is Transcript"'
+    }
+}
diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
index 8626a663..00a03673 100644
--- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
+++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
@@ -1,25 +1,34 @@
 Changes in module 'nf-core/ensemblvep/vep'
+'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged
+Changes in 'ensemblvep/vep/main.nf':
 --- modules/nf-core/ensemblvep/vep/main.nf
 +++ modules/nf-core/ensemblvep/vep/main.nf
 @@ -4,8 +4,8 @@
  
      conda "${moduleDir}/environment.yml"
      container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' :
--        'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }"
+-        'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
+-        'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
 +        'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' :
 +        'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }"
  
      input:
      tuple val(meta), path(vcf), path(custom_extra_files)
 
+Changes in 'ensemblvep/vep/environment.yml':
 --- modules/nf-core/ensemblvep/vep/environment.yml
 +++ modules/nf-core/ensemblvep/vep/environment.yml
-@@ -4,4 +4,4 @@
+@@ -2,4 +2,4 @@
+   - conda-forge
    - bioconda
-   - defaults
  dependencies:
--  - bioconda::ensembl-vep=111.0
+-  - bioconda::ensembl-vep=113.0
 +  - bioconda::ensembl-vep=110.0
 
+'modules/nf-core/ensemblvep/vep/tests/tags.yml' is unchanged
+'modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/ensemblvep/vep/tests/nextflow.config' is unchanged
+'modules/nf-core/ensemblvep/vep/tests/tab.gz.config' is unchanged
+'modules/nf-core/ensemblvep/vep/tests/main.nf.test' is unchanged
+'modules/nf-core/ensemblvep/vep/tests/vcf.config' is unchanged
 ************************************************************
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
index 7a127746..bf25a4da 100644
--- a/modules/nf-core/ensemblvep/vep/environment.yml
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -1,7 +1,5 @@
-name: ensemblvep_vep
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::ensembl-vep=110.0
diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml
index d8ff8d14..9288a938 100644
--- a/modules/nf-core/ensemblvep/vep/meta.yml
+++ b/modules/nf-core/ensemblvep/vep/meta.yml
@@ -1,5 +1,6 @@
 name: ensemblvep_vep
-description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
+description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled
+  through `task.ext.args`.
 keywords:
   - annotation
   - vcf
@@ -13,75 +14,96 @@ tools:
       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"]
+      identifier: ""
 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)
+  - - 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"
+      - meta:
+          type: file
+          description: |
+            annotated vcf (optional)
+          pattern: "*.ann.vcf.gz"
+      - "*.vcf.gz":
+          type: file
+          description: |
+            annotated vcf (optional)
+          pattern: "*.ann.vcf.gz"
   - tab:
-      type: file
-      description: |
-        tab file with annotated variants (optional)
-      pattern: "*.ann.tab.gz"
+      - meta:
+          type: file
+          description: |
+            tab file with annotated variants (optional)
+          pattern: "*.ann.tab.gz"
+      - "*.tab.gz":
+          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"
+      - meta:
+          type: file
+          description: |
+            json file with annotated variants (optional)
+          pattern: "*.ann.json.gz"
+      - "*.json.gz":
+          type: file
+          description: |
+            json file with annotated variants (optional)
+          pattern: "*.ann.json.gz"
   - report:
-      type: file
-      description: VEP report file
-      pattern: "*.html"
+      - "*.html":
+          type: file
+          description: VEP report file
+          pattern: "*.html"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@maxulysse"
   - "@matthdsm"
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
index 4aff84a3..3e8c0b53 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = Channel.of([
-                        [id:"111_WBcel235"],
+                        [id:"113_WBcel235"],
                         params.vep_genome,
                         params.vep_species,
                         params.vep_cache_version
@@ -72,7 +72,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = Channel.of([
-                        [id:"111_WBcel235"],
+                        [id:"113_WBcel235"],
                         params.vep_genome,
                         params.vep_species,
                         params.vep_cache_version
@@ -107,7 +107,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.versions).match() },
-                { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v111.0") }
+                { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") }
             )
         }
     }
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
index f937b299..1df94276 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
@@ -2,25 +2,25 @@
     "test_ensemblvep_vep_fasta_tab_gz": {
         "content": [
             [
-                "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba"
+                "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-15T17:35:20.694114"
+        "timestamp": "2024-10-21T09:12:23.474703494"
     },
     "test_ensemblvep_vep_fasta_vcf": {
         "content": [
             [
-                "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba"
+                "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-15T17:34:41.093843"
+        "timestamp": "2024-10-21T09:11:54.343590485"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
index 882bce41..0a4ae1a6 100644
--- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config
+++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
@@ -1,5 +1,5 @@
 params {
-    vep_cache_version   = "111"
+    vep_cache_version   = "113"
     vep_genome          = "WBcel235"
     vep_species         = "caenorhabditis_elegans"
 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38a..691d4c76 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c86..d8989f48 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e0..4827da7a 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4d..e9d79a07 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ 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[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") }
+                { 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[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() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         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") }
+                { 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() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         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") }
+                { 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() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         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") }
+                { 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() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         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") }
+                { 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() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         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") }
+                { 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() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         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") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c311..d5db3092 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml
index 3d98a08b..315f6dc6 100644
--- a/modules/nf-core/gawk/environment.yml
+++ b/modules/nf-core/gawk/environment.yml
@@ -1,7 +1,5 @@
-name: gawk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::gawk=5.3.0
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
index ca468929..7514246e 100644
--- a/modules/nf-core/gawk/main.nf
+++ b/modules/nf-core/gawk/main.nf
@@ -8,7 +8,7 @@ process GAWK {
         'biocontainers/gawk:5.3.0' }"
 
     input:
-    tuple val(meta), path(input)
+    tuple val(meta), path(input, arity: '0..*')
     path(program_file)
 
     output:
@@ -22,15 +22,19 @@ process GAWK {
     def args  = task.ext.args  ?: '' // args is used for the main arguments of the tool
     def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given
     prefix = task.ext.prefix ?: "${meta.id}"
-    suffix = task.ext.suffix ?: "${input.getExtension()}"
+    suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
 
-    program = program_file ? "-f ${program_file}" : "${args2}"
+    program   = program_file ? "-f ${program_file}" : "${args2}"
+    lst_gz    = input.collect{ it.getExtension().endsWith("gz") }
+    unzip     = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\"
+    input_cmd = unzip ? "" : "${input}"
 
     """
+    ${unzip}
     awk \\
         ${args} \\
         ${program} \\
-        ${input} \\
+        ${input_cmd} \\
         > ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml
index 2b6033b0..2da41405 100644
--- a/modules/nf-core/gawk/meta.yml
+++ b/modules/nf-core/gawk/meta.yml
@@ -16,34 +16,41 @@ tools:
       documentation: "https://www.gnu.org/software/gawk/manual/"
       tool_dev_url: "https://www.gnu.org/prep/ftp.html"
       licence: ["GPL v3"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file
-      pattern: "*"
-  - program_file:
-      type: file
-      description: Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic.
-      pattern: "*"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: The input file - Specify the logic that needs to be executed on
+          this file on the `ext.args2` or in the program file.
+          If the files have a `.gz` extension, they will be unzipped using `zcat`.
+        pattern: "*"
+  - - program_file:
+        type: file
+        description: Optional file containing logic for awk to execute. If you don't
+          wish to use a file, you can use `ext.args2` to specify the logic.
+        pattern: "*"
 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"
   - output:
-      type: file
-      description: The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix`
-      pattern: "*"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.${suffix}:
+          type: file
+          description: The output file - specify the name of this file using `ext.prefix`
+            and the extension using `ext.suffix`
+          pattern: "*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test
index fce82ca9..5952e9a2 100644
--- a/modules/nf-core/gawk/tests/main.nf.test
+++ b/modules/nf-core/gawk/tests/main.nf.test
@@ -8,7 +8,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "gawk"
 
-    test("convert fasta to bed") {
+    test("Convert fasta to bed") {
         config "./nextflow.config"
 
         when {
@@ -31,7 +31,7 @@ nextflow_process {
         }
     }
 
-    test("convert fasta to bed with program file") {
+    test("Convert fasta to bed with program file") {
         config "./nextflow_with_program_file.config"
 
         when {
@@ -53,4 +53,52 @@ nextflow_process {
             )
         }
     }
+
+    test("Extract first column from multiple files") {
+        config "./nextflow_with_program_file.config"
+        tag "test"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)]
+                ]
+                input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.txt")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Unzip files before processing") {
+        config "./nextflow_with_program_file.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)]
+                ]
+                input[1] = Channel.of('/^#CHROM/ { print \$1, \$10 }').collectFile(name:"column_header.txt")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap
index 4f3a759c..d396f738 100644
--- a/modules/nf-core/gawk/tests/main.nf.test.snap
+++ b/modules/nf-core/gawk/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "convert fasta to bed with program file": {
+    "Convert fasta to bed": {
         "content": [
             {
                 "0": [
@@ -28,11 +28,11 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-17T15:20:02.495430346"
+        "timestamp": "2024-10-19T13:14:02.347809811"
     },
-    "convert fasta to bed": {
+    "Convert fasta to bed with program file": {
         "content": [
             {
                 "0": [
@@ -61,8 +61,74 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-17T15:19:53.291809648"
+        "timestamp": "2024-10-19T13:14:11.894616209"
+    },
+    "Extract first column from multiple files": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,566c51674bd643227bb2d83e0963376d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,566c51674bd643227bb2d83e0963376d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-19T22:04:47.729300129"
+    },
+    "Unzip files before processing": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-19T22:08:19.533527657"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
index ac8140fd..227ee892 100644
--- a/modules/nf-core/genmod/annotate/environment.yml
+++ b/modules/nf-core/genmod/annotate/environment.yml
@@ -1,7 +1,5 @@
-name: genmod_annotate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
index eb161187..0b8b232d 100644
--- a/modules/nf-core/genmod/annotate/main.nf
+++ b/modules/nf-core/genmod/annotate/main.nf
@@ -4,15 +4,15 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_annotate.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml
index 3c876ac5..bb4afb6b 100644
--- a/modules/nf-core/genmod/annotate/meta.yml
+++ b/modules/nf-core/genmod/annotate/meta.yml
@@ -11,30 +11,33 @@ tools:
       documentation: "https://github.com/Clinical-Genomics/genmod"
       tool_dev_url: "https://github.com/moonso"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_vcf:
-      type: file
-      description: VCF file
-      pattern: "*.{vcf}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_vcf:
+        type: file
+        description: VCF file
+        pattern: "*.{vcf}"
 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"
   - vcf:
-      type: file
-      description: Annotated VCF file
-      pattern: "*.{vcf}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_annotate.vcf":
+          type: file
+          description: Annotated VCF file
+          pattern: "*.{vcf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test
index d17ebc9e..a4b3fccb 100644
--- a/modules/nf-core/genmod/annotate/tests/main.nf.test
+++ b/modules/nf-core/genmod/annotate/tests/main.nf.test
@@ -24,8 +24,35 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("genmod_annotate - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
new file mode 100644
index 00000000..402b5c01
--- /dev/null
+++ b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_annotate": {
+        "content": [
+            [
+                "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+            ],
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:44:57.176895794"
+    },
+    "genmod_annotate - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6ce3597967a536ab027d02f75d02056c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:16.409331019"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
index 1e2561fd..227ee892 100644
--- a/modules/nf-core/genmod/compound/environment.yml
+++ b/modules/nf-core/genmod/compound/environment.yml
@@ -1,7 +1,5 @@
-name: genmod_compound
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
index 1731b722..ca6a22a1 100644
--- a/modules/nf-core/genmod/compound/main.nf
+++ b/modules/nf-core/genmod/compound/main.nf
@@ -4,15 +4,15 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_compound.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml
index aa5f7da5..ebd6a110 100644
--- a/modules/nf-core/genmod/compound/meta.yml
+++ b/modules/nf-core/genmod/compound/meta.yml
@@ -11,30 +11,33 @@ tools:
       documentation: "https://github.com/Clinical-Genomics/genmod"
       tool_dev_url: "https://github.com/moonso"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_vcf:
-      type: file
-      description: VCF file
-      pattern: "*.{vcf}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_vcf:
+        type: file
+        description: VCF file
+        pattern: "*.{vcf}"
 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"
   - vcf:
-      type: file
-      description: Output VCF file
-      pattern: "*.{vcf}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]  #
+      - "*_compound.vcf":
+          type: file
+          description: Output VCF file
+          pattern: "*.{vcf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test
index 43ed9f0d..4c667c17 100644
--- a/modules/nf-core/genmod/compound/tests/main.nf.test
+++ b/modules/nf-core/genmod/compound/tests/main.nf.test
@@ -23,8 +23,35 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("genmod_compound - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test.snap b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
new file mode 100644
index 00000000..b114cc33
--- /dev/null
+++ b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_compound": {
+        "content": [
+            [
+                "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+            ],
+            "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:41.417545149"
+    },
+    "genmod_compound - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,822fb501a48a6f8c28ba8f678d27ba2e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:48.678803012"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
index 62a746c7..227ee892 100644
--- a/modules/nf-core/genmod/models/environment.yml
+++ b/modules/nf-core/genmod/models/environment.yml
@@ -1,7 +1,5 @@
-name: genmod_models
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
index 0504574a..a869221e 100644
--- a/modules/nf-core/genmod/models/main.nf
+++ b/modules/nf-core/genmod/models/main.nf
@@ -4,17 +4,16 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input_vcf)
-    path (fam)
+    tuple val(meta), path(input_vcf), path (fam)
     path (reduced_penetrance)
 
     output:
     tuple val(meta), path("*_models.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml
index dd9001e0..a6249114 100644
--- a/modules/nf-core/genmod/models/meta.yml
+++ b/modules/nf-core/genmod/models/meta.yml
@@ -11,38 +11,40 @@ tools:
       documentation: "https://github.com/Clinical-Genomics/genmod"
       tool_dev_url: "https://github.com/moonso"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_vcf:
-      type: file
-      description: vcf file
-      pattern: "*.{vcf}"
-  - reduced_penetrance:
-      type: file
-      description: file with gene ids that have reduced penetrance
-      pattern: "*.{tsv}"
-  - family_file:
-      type: file
-      description: ped file
-      pattern: "*.{ped}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_vcf:
+        type: file
+        description: vcf file
+        pattern: "*.{vcf}"
+    - fam:
+        type: file
+        description: PED file with family information
+  - - reduced_penetrance:
+        type: file
+        description: file with gene ids that have reduced penetrance
+        pattern: "*.{tsv}"
 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"
   - vcf:
-      type: file
-      description: Output VCF file
-      pattern: "*.{vcf}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_models.vcf":
+          type: file
+          description: Output VCF file
+          pattern: "*.{vcf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test
index 9eba8dd5..0b9a3ebd 100644
--- a/modules/nf-core/genmod/models/tests/main.nf.test
+++ b/modules/nf-core/genmod/models/tests/main.nf.test
@@ -15,21 +15,49 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = []
+                input[1] = []
                 """
             }
         }
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
             )
         }
 
     }
 
+    test("genmod_models - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 }
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test.snap b/modules/nf-core/genmod/models/tests/main.nf.test.snap
new file mode 100644
index 00000000..7484a7fd
--- /dev/null
+++ b/modules/nf-core/genmod/models/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_models - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:51:04.841425679"
+    },
+    "genmod_models": {
+        "content": [
+            [
+                "versions.yml:md5,10442b1602069000967f51837d7b5b63"
+            ],
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:49:56.642318737"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
index bacc4cec..227ee892 100644
--- a/modules/nf-core/genmod/score/environment.yml
+++ b/modules/nf-core/genmod/score/environment.yml
@@ -1,7 +1,5 @@
-name: genmod_score
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::genmod=3.8.2
+  - bioconda::genmod=3.9
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
index 15be5f74..756fc731 100644
--- a/modules/nf-core/genmod/score/main.nf
+++ b/modules/nf-core/genmod/score/main.nf
@@ -4,17 +4,16 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0':
-        'biocontainers/genmod:3.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0':
+        'biocontainers/genmod:3.9--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input_vcf)
-    path (fam)
+    tuple val(meta), path(input_vcf), path (fam)
     path (score_config)
 
     output:
     tuple val(meta), path("*_score.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml
index 8998b00c..c5fe2e2a 100644
--- a/modules/nf-core/genmod/score/meta.yml
+++ b/modules/nf-core/genmod/score/meta.yml
@@ -11,38 +11,40 @@ tools:
       documentation: "https://github.com/Clinical-Genomics/genmod"
       tool_dev_url: "https://github.com/moonso"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_vcf:
-      type: file
-      description: vcf file
-      pattern: "*.{vcf}"
-  - family_file:
-      type: file
-      description: ped file
-      pattern: "*.{ped}"
-  - score_config:
-      type: file
-      description: rank model config file
-      pattern: "*.{ini}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_vcf:
+        type: file
+        description: vcf file
+        pattern: "*.{vcf}"
+    - fam:
+        type: file
+        description: PED file with family information
+  - - score_config:
+        type: file
+        description: rank model config file
+        pattern: "*.{ini}"
 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"
   - vcf:
-      type: file
-      description: Output VCF file
-      pattern: "*.{vcf}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_score.vcf":
+          type: file
+          description: Output VCF file
+          pattern: "*.{vcf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test
index 030ef6ba..6181f63a 100644
--- a/modules/nf-core/genmod/score/tests/main.nf.test
+++ b/modules/nf-core/genmod/score/tests/main.nf.test
@@ -15,18 +15,47 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
-                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
                 """
             }
         }
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.2")}
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("genmod_score - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test.snap b/modules/nf-core/genmod/score/tests/main.nf.test.snap
new file mode 100644
index 00000000..b484b8e1
--- /dev/null
+++ b/modules/nf-core/genmod/score/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "genmod_score": {
+        "content": [
+            [
+                "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+            ],
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:50:12.03483811"
+    },
+    "genmod_score - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_score.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_score.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f310225b3c35456e84d52e2c400e2fd8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-25T11:50:19.675962486"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml
index 1c875ce0..b47bbdbb 100644
--- a/modules/nf-core/gfastats/environment.yml
+++ b/modules/nf-core/gfastats/environment.yml
@@ -1,7 +1,5 @@
-name: gfastats
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::gfastats=1.3.6
diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml
index d0e97a8f..a6213433 100644
--- a/modules/nf-core/gfastats/meta.yml
+++ b/modules/nf-core/gfastats/meta.yml
@@ -16,56 +16,67 @@ tools:
       documentation: "https://github.com/vgl-hub/gfastats/tree/main/instructions"
       tool_dev_url: "https://github.com/vgl-hub/gfastats"
       doi: "10.1093/bioinformatics/btac460"
-      licence: "['MIT']"
+      licence: ["MIT"]
+      identifier: biotools:gfastats
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - assembly:
-      type: file
-      description: Draft assembly file
-      pattern: "*.{fasta,fastq,gfa}(.gz)?"
-  - out_fmt:
-      type: string
-      description: Output format (fasta, fastq, gfa)
-  - genome_size:
-      type: integer
-      description: estimated genome size (bp) for NG* statistics (optional).
-  - target:
-      type: string
-      description: target specific sequence by header, optionally with coordinates (optional).
-  - agpfile:
-      type: file
-      description: converts input agp to path and replaces existing paths.
-  - include_bed:
-      type: file
-      description: generates output on a subset list of headers or coordinates in 0-based bed format.
-  - exclude_bed:
-      type: file
-      description: opposite of --include-bed. They can be combined (no coordinates).
-  - instructions:
-      type: file
-      description: set of instructions provided as an ordered list.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - assembly:
+        type: file
+        description: Draft assembly file
+        pattern: "*.{fasta,fastq,gfa}(.gz)?"
+  - - out_fmt:
+        type: string
+        description: Output format (fasta, fastq, gfa)
+  - - genome_size:
+        type: integer
+        description: estimated genome size (bp) for NG* statistics (optional).
+  - - target:
+        type: string
+        description: target specific sequence by header, optionally with coordinates
+          (optional).
+  - - agpfile:
+        type: file
+        description: converts input agp to path and replaces existing paths.
+  - - include_bed:
+        type: file
+        description: generates output on a subset list of headers or coordinates in
+          0-based bed format.
+  - - exclude_bed:
+        type: file
+        description: opposite of --include-bed. They can be combined (no coordinates).
+  - - instructions:
+        type: file
+        description: set of instructions provided as an ordered list.
 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"
   - assembly_summary:
-      type: file
-      description: Assembly summary statistics file
-      pattern: "*.assembly_summary"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.assembly_summary":
+          type: file
+          description: Assembly summary statistics file
+          pattern: "*.assembly_summary"
   - assembly:
-      type: file
-      description: The assembly as modified by gfastats
-      pattern: "*.{fasta,fastq,gfa}.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${out_fmt}.gz":
+          type: file
+          description: The assembly as modified by gfastats
+          pattern: "*.{fasta,fastq,gfa}.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@mahesh-panchal"
 maintainers:
diff --git a/modules/nf-core/glnexus/environment.yml b/modules/nf-core/glnexus/environment.yml
index 922214e8..9190508a 100644
--- a/modules/nf-core/glnexus/environment.yml
+++ b/modules/nf-core/glnexus/environment.yml
@@ -1,7 +1,5 @@
-name: glnexus
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::glnexus=1.4.1
diff --git a/modules/nf-core/glnexus/glnexus.diff b/modules/nf-core/glnexus/glnexus.diff
index c5bc3382..8684c709 100644
--- a/modules/nf-core/glnexus/glnexus.diff
+++ b/modules/nf-core/glnexus/glnexus.diff
@@ -1,39 +1,21 @@
 Changes in module 'nf-core/glnexus'
+'modules/nf-core/glnexus/meta.yml' is unchanged
+Changes in 'glnexus/main.nf':
 --- modules/nf-core/glnexus/main.nf
 +++ modules/nf-core/glnexus/main.nf
-@@ -1,14 +1,13 @@
- process GLNEXUS {
-     tag "$meta.id"
--    label 'process_medium'
-+    label 'process_high'
+@@ -3,9 +3,7 @@
+     label 'process_high'
  
      conda "${moduleDir}/environment.yml"
 -    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
 -        'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' :
 -        'biocontainers/glnexus:1.4.1--h40d77a6_0' }"
-+    container "pacbio/glnexus:v1.4.3" // Biocontainers version does not have jemalloc 
++    container "pacbio/glnexus:v1.4.3" // Biocontainers version does not have jemalloc
  
      input:
      tuple val(meta), path(gvcfs)
-+    tuple val(meta2), path(bed)
- 
-     output:
-     tuple val(meta), path("*.bcf"), emit: bcf
-@@ -20,6 +19,7 @@
-     script:
-     def args = task.ext.args ?: ''
-     def prefix = task.ext.prefix ?: "${meta.id}"
-+    def regions = bed ? "--bed ${bed}" : ""
- 
-     // Make list of GVCFs to merge
-     def input = gvcfs.collect { it.toString() }
-@@ -33,6 +33,7 @@
-     glnexus_cli \\
-         --threads $task.cpus \\
-         --mem-gbytes $avail_mem \\
-+        $regions \\
-         $args \\
-         ${input.join(' ')} \\
-         > ${prefix}.bcf
 
+'modules/nf-core/glnexus/environment.yml' is unchanged
+'modules/nf-core/glnexus/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/glnexus/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf
index 6147d71d..59857115 100644
--- a/modules/nf-core/glnexus/main.nf
+++ b/modules/nf-core/glnexus/main.nf
@@ -3,7 +3,7 @@ process GLNEXUS {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "pacbio/glnexus:v1.4.3" // Biocontainers version does not have jemalloc 
+    container "pacbio/glnexus:v1.4.3" // Biocontainers version does not have jemalloc
 
     input:
     tuple val(meta), path(gvcfs)
diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml
index 4944ebde..8f18bf3f 100644
--- a/modules/nf-core/glnexus/meta.yml
+++ b/modules/nf-core/glnexus/meta.yml
@@ -3,32 +3,50 @@ description: merge gVCF files and perform joint variant calling
 keywords:
   - merge
   - gvcf
+  - joint-variant-calling
 tools:
   - glnexus:
-      description: scalable gVCF merging and joint variant calling for population sequencing projects.
+      description: scalable gVCF merging and joint variant calling for population sequencing
+        projects.
       homepage: https://github.com/dnanexus-rnd/GLnexus
       documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
       doi: 10.1101/343970
       licence: ["Apache-2.0"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - gvcfs:
-      type: list
-      description: Input genomic vcf files
-      pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - gvcfs:
+        type: list
+        description: Input genomic vcf files
+        pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions information
+          e.g. [ id:'test' ]
+    - bed:
+        type: list
+        description: Input BED file
+        pattern: "*.bed"
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - bcf:
-      type: file
-      description: merged BCF file
-      pattern: "*.bcf"
+      - meta:
+          type: file
+          description: merged BCF file
+          pattern: "*.bcf"
+      - "*.bcf":
+          type: file
+          description: merged BCF file
+          pattern: "*.bcf"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/glnexus/tests/main.nf.test b/modules/nf-core/glnexus/tests/main.nf.test
new file mode 100644
index 00000000..79f7adc8
--- /dev/null
+++ b/modules/nf-core/glnexus/tests/main.nf.test
@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process GLNEXUS"
+    script "../main.nf"
+    process "GLNEXUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "glnexus"
+
+    test("vcfs, []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/glnexus/tests/main.nf.test.snap b/modules/nf-core/glnexus/tests/main.nf.test.snap
new file mode 100644
index 00000000..3d2e13f0
--- /dev/null
+++ b/modules/nf-core/glnexus/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "vcfs, bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:17:01.253378301"
+    },
+    "vcfs, bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:16:53.859544065"
+    },
+    "vcfs, []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:13:03.068397129"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
index dfc02a7b..c7794856 100644
--- a/modules/nf-core/gunzip/environment.yml
+++ b/modules/nf-core/gunzip/environment.yml
@@ -1,8 +1,6 @@
-name: gunzip
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::grep=3.11
   - conda-forge::sed=4.8
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
index f32973a0..9066c035 100644
--- a/modules/nf-core/gunzip/meta.yml
+++ b/modules/nf-core/gunzip/meta.yml
@@ -10,25 +10,32 @@ tools:
         gzip is a file format and a software application used for file compression and decompression.
       documentation: https://www.gnu.org/software/gzip/manual/gzip.html
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Optional groovy Map containing meta information
-        e.g. [ id:'test', single_end:false ]
-  - archive:
-      type: file
-      description: File to be compressed/uncompressed
-      pattern: "*.*"
+  - - meta:
+        type: map
+        description: |
+          Optional groovy Map containing meta information
+          e.g. [ id:'test', single_end:false ]
+    - archive:
+        type: file
+        description: File to be compressed/uncompressed
+        pattern: "*.*"
 output:
   - gunzip:
-      type: file
-      description: Compressed/uncompressed file
-      pattern: "*.*"
+      - meta:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
+      - $gunzip:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml
index ede93247..f50b420e 100644
--- a/modules/nf-core/hifiasm/environment.yml
+++ b/modules/nf-core/hifiasm/environment.yml
@@ -1,7 +1,5 @@
-name: hifiasm
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::hifiasm=0.19.8
+  - bioconda::hifiasm=0.20.0
diff --git a/modules/nf-core/hifiasm/hifiasm.diff b/modules/nf-core/hifiasm/hifiasm.diff
index 03790816..0d5e8ef7 100644
--- a/modules/nf-core/hifiasm/hifiasm.diff
+++ b/modules/nf-core/hifiasm/hifiasm.diff
@@ -1,16 +1,24 @@
 Changes in module 'nf-core/hifiasm'
+'modules/nf-core/hifiasm/meta.yml' is unchanged
+'modules/nf-core/hifiasm/environment.yml' is unchanged
+Changes in 'hifiasm/main.nf':
 --- modules/nf-core/hifiasm/main.nf
 +++ modules/nf-core/hifiasm/main.nf
-@@ -8,9 +8,7 @@
-         'biocontainers/hifiasm:0.19.8--h43eeafb_0' }"
+@@ -8,9 +8,9 @@
+         'biocontainers/hifiasm:0.20.0--h43eeafb_0' }"
  
      input:
--    tuple val(meta), path(reads)
--    path  paternal_kmer_dump
--    path  maternal_kmer_dump
-+    tuple val(meta), path(reads, stageAs: "?/*"), path(paternal_kmer_dump), path(maternal_kmer_dump)
-     path  hic_read1
-     path  hic_read2
+-    tuple val(meta) , path(reads)
+-    tuple val(meta1), path(paternal_kmer_dump), path(maternal_kmer_dump)
+-    tuple val(meta2), path(hic_read1)         , path(hic_read2)
++    tuple val(meta) , path(reads, stageAs: "?/*")
++    tuple val(meta1), path(paternal_kmer_dump)   , path(maternal_kmer_dump)
++    tuple val(meta2), path(hic_read1)            , path(hic_read2)
  
+     output:
+     tuple val(meta), path("*.r_utg.gfa")       , emit: raw_unitigs
 
+'modules/nf-core/hifiasm/tests/main.nf.test' is unchanged
+'modules/nf-core/hifiasm/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/hifiasm/tests/nextflow.config' is unchanged
 ************************************************************
diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
index a1bf30a0..409f7704 100644
--- a/modules/nf-core/hifiasm/main.nf
+++ b/modules/nf-core/hifiasm/main.nf
@@ -4,13 +4,13 @@ process HIFIASM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hifiasm:0.19.8--h43eeafb_0' :
-        'biocontainers/hifiasm:0.19.8--h43eeafb_0' }"
+        'https://depot.galaxyproject.org/singularity/hifiasm:0.20.0--h43eeafb_0' :
+        'biocontainers/hifiasm:0.20.0--h43eeafb_0' }"
 
     input:
-    tuple val(meta), path(reads, stageAs: "?/*"), path(paternal_kmer_dump), path(maternal_kmer_dump)
-    path  hic_read1
-    path  hic_read2
+    tuple val(meta) , path(reads, stageAs: "?/*")
+    tuple val(meta1), path(paternal_kmer_dump)   , path(maternal_kmer_dump)
+    tuple val(meta2), path(hic_read1)            , path(hic_read2)
 
     output:
     tuple val(meta), path("*.r_utg.gfa")       , emit: raw_unitigs
diff --git a/modules/nf-core/hifiasm/meta.yml b/modules/nf-core/hifiasm/meta.yml
index d07c0828..343ef182 100644
--- a/modules/nf-core/hifiasm/meta.yml
+++ b/modules/nf-core/hifiasm/meta.yml
@@ -15,85 +15,160 @@ tools:
       tool_dev_url: https://github.com/chhylp123/hifiasm
       doi: "10.1038/s41592-020-01056-5"
       licence: ["MIT"]
+      identifier: biotools:hifiasm
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: FASTQ file with PacBio HiFi reads
-      pattern: "*.{fastq}"
-  - paternal_kmer_dump:
-      type: file
-      description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
-  - maternal_kmer_dump:
-      type: file
-      description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
-  - use_parental_kmers:
-      type: boolean
-      description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps.
-  - hic_read1:
-      type: file
-      description: Hi-C data Forward reads.
-  - hic_read2:
-      type: file
-      description: Hi-C data Reverse reads.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: FASTQ file with PacBio HiFi reads
+        pattern: "*.{fastq}"
+  - - meta1:
+        type: map
+        description: |
+          Groovy Map containing information about parental kmers.
+    - paternal_kmer_dump:
+        type: file
+        description: Yak kmer dump file for paternal reads (can be used for haplotype
+          resolution). It can have an arbitrary extension.
+    - maternal_kmer_dump:
+        type: file
+        description: Yak kmer dump file for maternal reads (can be used for haplotype
+          resolution). It can have an arbitrary extension.
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing information about Hi-C reads
+    - hic_read1:
+        type: file
+        description: Hi-C data Forward reads.
+    - hic_read2:
+        type: file
+        description: Hi-C data Reverse reads.
 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"
   - raw_unitigs:
-      type: file
-      description: Raw unitigs
-      pattern: "*.r_utg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.r_utg.gfa":
+          type: file
+          description: Raw unitigs
+          pattern: "*.r_utg.gfa"
+  - corrected_reads:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ec.bin":
+          type: file
+          description: Corrected reads
+          pattern: "*.ec.bin"
+  - source_overlaps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ovlp.source.bin":
+          type: file
+          description: Source overlaps
+          pattern: "*.ovlp.source.bin"
+  - reverse_overlaps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ovlp.reverse.bin":
+          type: file
+          description: Reverse overlaps
+          pattern: "*.ovlp.reverse.bin"
+  - processed_contigs:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bp.p_ctg.gfa":
+          type: file
+          description: Processed contigs
+          pattern: "*.bp.p_ctg.gfa"
   - processed_unitigs:
-      type: file
-      description: Processed unitigs
-      pattern: "*.p_utg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.p_utg.gfa":
+          type: file
+          description: Processed unitigs
+          pattern: "*.p_utg.gfa"
   - primary_contigs:
-      type: file
-      description: Primary contigs
-      pattern: "*.asm.p_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.asm.p_ctg.gfa":
+          type: file
+          description: Primary contigs
+          pattern: "*.asm.p_ctg.gfa"
   - alternate_contigs:
-      type: file
-      description: Alternative contigs
-      pattern: "*.asm.a_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.asm.a_ctg.gfa":
+          type: file
+          description: Alternative contigs
+          pattern: "*.asm.a_ctg.gfa"
   - paternal_contigs:
-      type: file
-      description: Paternal contigs
-      pattern: "*.hap1.p_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.hap1.p_ctg.gfa":
+          type: file
+          description: Paternal contigs
+          pattern: "*.hap1.p_ctg.gfa"
   - maternal_contigs:
-      type: file
-      description: Maternal contigs
-      pattern: "*.hap2.p_ctg.gfa"
-  - corrected_reads:
-      type: file
-      description: Corrected reads
-      pattern: "*.ec.bin"
-  - source_overlaps:
-      type: file
-      description: Source overlaps
-      pattern: "*.ovlp.source.bin"
-  - reverse_overlaps:
-      type: file
-      description: Reverse overlaps
-      pattern: "*.ovlp.reverse.bin"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.hap2.p_ctg.gfa":
+          type: file
+          description: Maternal contigs
+          pattern: "*.hap2.p_ctg.gfa"
   - log:
-      type: file
-      description: Stderr log
-      pattern: "*.log"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.log":
+          type: file
+          description: Stderr log
+          pattern: "*.log"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@sidorov-si"
   - "@scorreard"
   - "@mbeavitt"
+  - "@schmytzi"
 maintainers:
   - "@sidorov-si"
   - "@scorreard"
diff --git a/modules/nf-core/hifiasm/tests/main.nf.test b/modules/nf-core/hifiasm/tests/main.nf.test
new file mode 100644
index 00000000..5258890a
--- /dev/null
+++ b/modules/nf-core/hifiasm/tests/main.nf.test
@@ -0,0 +1,229 @@
+nextflow_process {
+
+    name "Test Process HifiAsm"
+    script "../main.nf"
+    process "HIFIASM"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hifiasm"
+
+    test("homo_sapiens pacbio hifi [fastq, [,], [,] ]") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [],
+                    [],
+                    []
+                ]
+                input[2] = [
+                    [],
+                    [],
+                    []
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.corrected_reads.get(0).get(1)).exists() },
+                { assert file(process.out.source_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.log.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.raw_unitigs,
+                    process.out.processed_contigs,
+                    process.out.processed_unitigs,
+                    process.out.paternal_contigs,
+                    process.out.maternal_contigs,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [yak, yak], [,] ]") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id : 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test2.yak', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id : 'test' ],
+                    [],
+                    []
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.corrected_reads.get(0).get(1)).exists() },
+                { assert file(process.out.source_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.log.get(0).get(1)).exists() },
+                { assert file(process.out.maternal_contigs.get(0).get(1)).length() == 0},
+                { assert snapshot(
+                    process.out.raw_unitigs,
+                    process.out.processed_unitigs,
+                    process.out.paternal_contigs,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [,], [fastq, fastq] ]") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id : 'test' ],
+                    [],
+                    []
+                ]
+                input[2] = [
+                    [ id : 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.corrected_reads.get(0).get(1)).exists() },
+                { assert file(process.out.source_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() },
+                { assert file(process.out.log.get(0).get(1)).exists() },
+                { assert file(process.out.maternal_contigs.get(0).get(1)).length() == 0},
+                { assert snapshot(
+                    process.out.raw_unitigs,
+                    process.out.processed_unitigs,
+                    process.out.paternal_contigs,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [yak, yak], [fastq, fastq] ]") {
+        when {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id : 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test2.yak', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id : 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz, checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz, checkIfExists: true)
+                ]
+                """
+        }
+        then {
+            assertAll(
+                { assert !process.success}
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [yak, ], [,] ]") {
+        when {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true),
+                    []
+                ]
+                input[2] = []
+                """
+        }
+        then {
+            assertAll(
+                { assert !process.success}
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [,], [, fastq] ]") {
+        when {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = [
+                    [ id : 'test'],
+                    [],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                ]
+                """
+        }
+        then {
+            assertAll(
+                { assert !process.success}
+            )
+        }
+    }
+
+    test("homo_sapiens pacbio hifi [fastq, [,], [,] ] - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id : 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = [
+                    [],
+                    [],
+                    []
+                ]
+                input[2] = [
+                    [],
+                    [],
+                    []
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()}
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/hifiasm/tests/main.nf.test.snap b/modules/nf-core/hifiasm/tests/main.nf.test.snap
new file mode 100644
index 00000000..8ad9589e
--- /dev/null
+++ b/modules/nf-core/hifiasm/tests/main.nf.test.snap
@@ -0,0 +1,319 @@
+{
+    "homo_sapiens pacbio hifi [fastq, [,], [,] ]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.bp.r_utg.gfa:md5,6a200e4bcb5d8d8fa6ed75874d26edc6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.bp.p_ctg.gfa:md5,c3225425a73a8d6d46536dab72380650"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.bp.p_utg.gfa:md5,6a200e4bcb5d8d8fa6ed75874d26edc6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.bp.hap1.p_ctg.gfa:md5,78a86b6d5741a680e22a427ca9faa74a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.bp.hap2.p_ctg.gfa:md5,ac2116fd2f22c67d4c304cbf9b9f7793"
+                ]
+            ],
+            [
+                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-23T14:01:04.528764919"
+    },
+    "homo_sapiens pacbio hifi [fastq, [,], [fastq, fastq] ]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.hic.r_utg.gfa:md5,6a200e4bcb5d8d8fa6ed75874d26edc6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.hic.p_utg.gfa:md5,6a200e4bcb5d8d8fa6ed75874d26edc6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.hic.hap1.p_ctg.gfa:md5,f67a8fdfa756961360732c79d189054d"
+                ]
+            ],
+            [
+                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-23T14:08:48.081396092"
+    },
+    "homo_sapiens pacbio hifi [fastq, [,], [,] ] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.r_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ec.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stderr.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "11": [
+                    "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ovlp.source.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ovlp.reverse.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.bp.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.p_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.a_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.hap1.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "alternate_contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.a_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "corrected_reads": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ec.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stderr.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "maternal_contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "paternal_contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.hap1.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "primary_contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "processed_contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.bp.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "processed_unitigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.p_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "raw_unitigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.r_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reverse_overlaps": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ovlp.reverse.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "source_overlaps": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.asm.ovlp.source.bin:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-23T14:09:13.475508542"
+    },
+    "homo_sapiens pacbio hifi [fastq, [yak, yak], [,] ]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.dip.r_utg.gfa:md5,68361ac3e8babd51f3891d1637ca0fdc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.dip.p_utg.gfa:md5,68361ac3e8babd51f3891d1637ca0fdc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.asm.dip.hap1.p_ctg.gfa:md5,eed5da5f3dd415dbb711edb61a09802f"
+                ]
+            ],
+            [
+                "versions.yml:md5,6a23f7ea8bae71905c537cd521cffcb8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-23T13:33:47.765243676"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/hifiasm/tests/nextflow.config b/modules/nf-core/hifiasm/tests/nextflow.config
new file mode 100644
index 00000000..8dc2ae48
--- /dev/null
+++ b/modules/nf-core/hifiasm/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-f0"
+}
diff --git a/modules/nf-core/longphase/haplotag/environment.yml b/modules/nf-core/longphase/haplotag/environment.yml
new file mode 100644
index 00000000..06445a93
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::longphase=1.7.3"
diff --git a/modules/nf-core/longphase/haplotag/main.nf b/modules/nf-core/longphase/haplotag/main.nf
new file mode 100644
index 00000000..86ba0592
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/main.nf
@@ -0,0 +1,66 @@
+process LONGPHASE_HAPLOTAG {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/longphase:1.7.3--hf5e1c6e_0':
+        'biocontainers/longphase:1.7.3--hf5e1c6e_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(snps), path(svs), path(mods)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+
+
+    output:
+    tuple val(meta), path("*.{bam,cram}"), emit: bam
+    tuple val(meta), path("*.log")       , emit: log , optional: true
+    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 sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
+
+    """
+    longphase \\
+        haplotag \\
+        $args \\
+        --threads $task.cpus \\
+        -o ${prefix} \\
+        --reference ${fasta} \\
+        --snp-file ${snps} \\
+        --bam ${bam} \\
+        ${sv_file} \\
+        ${mod_file}
+
+    if [ -f "${prefix}.out" ]; then
+        mv ${prefix}.out ${prefix}.log
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = args.contains('--cram') ? "cram" : "bam"
+    def log = args.contains('--log') ? "touch ${prefix}.log" : ''
+    """
+    touch ${prefix}.${suffix}
+    ${log}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/longphase/haplotag/meta.yml b/modules/nf-core/longphase/haplotag/meta.yml
new file mode 100644
index 00000000..d2f2ec8d
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/meta.yml
@@ -0,0 +1,94 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "longphase_haplotag"
+description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs,
+  small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
+keywords:
+  - haplotag
+  - long-read
+  - genomics
+tools:
+  - "longphase":
+      description: "LongPhase is an ultra-fast program for simultaneously co-phasing
+        SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio
+        platforms."
+      homepage: "https://github.com/twolinin/longphase"
+      documentation: "https://github.com/twolinin/longphase"
+      tool_dev_url: "https://github.com/twolinin/longphase"
+      doi: "10.1093/bioinformatics/btac058"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM file
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: Index of sorted BAM/CRAM file
+        pattern: "*.{bai,crai,csi}"
+    - snps:
+        type: file
+        description: VCF file with SNPs (and INDELs)
+        pattern: "*.{vcf,vcf.gz}"
+    - svs:
+        type: file
+        description: VCF file with SVs
+        pattern: "*.{vcf,vcf.gz}"
+    - mods:
+        type: file
+        description: modcall-generated VCF with modifications
+        pattern: "*.{vcf,vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'hg38' ]`
+    - fasta:
+        type: file
+        description: Reference fasta file
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'hg38' ]`
+    - fai:
+        type: file
+        description: Reference fai index
+        pattern: "*.fai"
+output:
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.{bam,cram}":
+          type: file
+          description: BAM file with haplotagged reads
+          pattern: "*.bam"
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.log":
+          type: file
+          description: Log file
+          pattern: "*.log"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"
diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test b/modules/nf-core/longphase/haplotag/tests/main.nf.test
new file mode 100644
index 00000000..c80133c6
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/tests/main.nf.test
@@ -0,0 +1,202 @@
+nextflow_process {
+
+    name "Test Process LONGPHASE_HAPLOTAG"
+    script "../main.nf"
+    process "LONGPHASE_HAPLOTAG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "longphase"
+    tag "longphase/haplotag"
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    bam(process.out.bam.get(0).get(1), stringency: 'silent').getHeader(),
+                    bam(process.out.bam.get(0).get(1), stringency: 'silent').getReadsMD5(),
+                ).match() }
+            )
+        }
+
+    }
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai - log & cram") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.log,
+                    bam(process.out.bam.get(0).get(1), 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/genome.fasta', stringency: 'silent').getHeader()[2..5],
+                    bam(process.out.bam.get(0).get(1), 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/genome.fasta', stringency: 'silent').getReadsMD5(),
+                ).match() }
+            )
+        }
+
+    }
+
+    test("[ bam, bai, snps, svs, [] ], fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    bam(process.out.bam.get(0).get(1), stringency: 'silent').getHeader(),
+                    bam(process.out.bam.get(0).get(1), stringency: 'silent').getReadsMD5(),
+                ).match() }
+            )
+        }
+
+    }
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai - log & cram -stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
new file mode 100644
index 00000000..3cf35dc3
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap
@@ -0,0 +1,159 @@
+{
+    "[ bam, bai, snps, [], [] ], fasta, fai - log & cram -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-09T09:40:30.738831707"
+    },
+    "[ bam, bai, snps, [], [] ], fasta, fai": {
+        "content": [
+            [
+                "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+            ],
+            [
+                "@HD\tVN:1.6\tSO:coordinate",
+                "@SQ\tSN:chr22\tLN:40001",
+                "@RG\tID:test\tSM:test",
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index",
+                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam "
+            ],
+            "721264eb2824a3146b331f2532d10180"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-25T09:12:34.848038423"
+    },
+    "[ bam, bai, snps, [], [] ], fasta, fai -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-09T09:40:20.836809553"
+    },
+    "[ bam, bai, snps, svs, [] ], fasta, fai": {
+        "content": [
+            [
+                "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+            ],
+            [
+                "@HD\tVN:1.6\tSO:coordinate",
+                "@SQ\tSN:chr22\tLN:40001",
+                "@RG\tID:test\tSM:test",
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index",
+                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam --sv-file NA24385_sv.vcf.gz "
+            ],
+            "721264eb2824a3146b331f2532d10180"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-04T13:39:33.50395694"
+    },
+    "[ bam, bai, snps, [], [] ], fasta, fai - log & cram": {
+        "content": [
+            [
+                "versions.yml:md5,3c169b598f6e15332b6d7ec1d6d96810"
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.log:md5,6203f10696f4b0909f0d327c021df773"
+                ]
+            ],
+            [
+                "@RG\tID:test\tSM:test",
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index",
+                "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --log --cram --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam "
+            ],
+            "721264eb2824a3146b331f2532d10180"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-25T09:45:54.254102844"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/longphase/haplotag/tests/nextflow.config b/modules/nf-core/longphase/haplotag/tests/nextflow.config
new file mode 100644
index 00000000..d50498b2
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'LONGPHASE_HAPLOTAG' {
+        ext.args = '--log --cram'
+    }
+}
diff --git a/modules/nf-core/longphase/haplotag/tests/tags.yml b/modules/nf-core/longphase/haplotag/tests/tags.yml
new file mode 100644
index 00000000..117e16a5
--- /dev/null
+++ b/modules/nf-core/longphase/haplotag/tests/tags.yml
@@ -0,0 +1,2 @@
+longphase/haplotag:
+  - "modules/nf-core/longphase/haplotag/**"
diff --git a/modules/nf-core/longphase/phase/environment.yml b/modules/nf-core/longphase/phase/environment.yml
new file mode 100644
index 00000000..bb2d0eee
--- /dev/null
+++ b/modules/nf-core/longphase/phase/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::htslib=1.20
+  - bioconda::longphase=1.7.3
diff --git a/modules/nf-core/longphase/phase/main.nf b/modules/nf-core/longphase/phase/main.nf
new file mode 100644
index 00000000..f121f4b6
--- /dev/null
+++ b/modules/nf-core/longphase/phase/main.nf
@@ -0,0 +1,69 @@
+process LONGPHASE_PHASE {
+    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/mulled-v2-d626bb8ec5a659accfbd8490bc1ac4a940722258:682e8c0cc0ceebf9bd38371a58249aabce93b1b3-0':
+        'biocontainers/mulled-v2-d626bb8ec5a659accfbd8490bc1ac4a940722258:682e8c0cc0ceebf9bd38371a58249aabce93b1b3-0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(snps), path(svs), path(mods)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def sv_file = svs ? "--sv-file ${svs}" : ""
+    def mod_file = mods ? "--mod-file ${mods}" : ""
+
+    def bamList = []
+    for (file in bam) {
+        bamList.add("-b")
+        bamList.add(file)
+    }
+    """
+    longphase \\
+        phase \\
+        $args \\
+        --threads $task.cpus \\
+        -o ${prefix} \\
+        --reference ${fasta} \\
+        --snp-file ${snps} \\
+        ${bamList.join(" ")} \\
+        ${sv_file} \\
+        ${mod_file} \\
+
+    bgzip \\
+        --threads $task.cpus \\
+        $args2 \\
+        ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | bgzip -c > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        longphase: \$(longphase --version | head -n 1 | sed 's/Version: //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/longphase/phase/meta.yml b/modules/nf-core/longphase/phase/meta.yml
new file mode 100644
index 00000000..823645d4
--- /dev/null
+++ b/modules/nf-core/longphase/phase/meta.yml
@@ -0,0 +1,84 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "longphase_phase"
+description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs,
+  small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
+keywords:
+  - phase
+  - long-read
+  - genomics
+tools:
+  - "longphase":
+      description: "LongPhase is an ultra-fast program for simultaneously co-phasing
+        SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio
+        platforms."
+      homepage: "https://github.com/twolinin/longphase"
+      documentation: "https://github.com/twolinin/longphase"
+      tool_dev_url: "https://github.com/twolinin/longphase"
+      doi: "10.1093/bioinformatics/btac058"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM file(s)
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: Index of sorted BAM/CRAM file(s)
+        pattern: "*.{bai,crai,csi}"
+    - snps:
+        type: file
+        description: VCF file with SNPs (and INDELs)
+        pattern: "*.{vcf,vcf.gz}"
+    - svs:
+        type: file
+        description: VCF file with SVs
+        pattern: "*.{vcf,vcf.gz}"
+    - mods:
+        type: file
+        description: modcall-generated VCF with modifications
+        pattern: "*.{vcf,vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'hg38' ]`
+    - fasta:
+        type: file
+        description: Reference fasta file
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'hg38' ]`
+    - fai:
+        type: file
+        description: Reference fai index
+        pattern: "*.fai"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: Compressed VCF file with phased variants
+          pattern: "*.vcf.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"
diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test b/modules/nf-core/longphase/phase/tests/main.nf.test
new file mode 100644
index 00000000..3e303312
--- /dev/null
+++ b/modules/nf-core/longphase/phase/tests/main.nf.test
@@ -0,0 +1,157 @@
+nextflow_process {
+
+    name "Test Process LONGPHASE_PHASE"
+    script "../main.nf"
+    process "LONGPHASE_PHASE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "longphase"
+    tag "longphase/phase"
+    config "./nextflow.config"
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+test("[ bam, bai, snps, svs, [] ], fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+test("[ bam x2, bai x2, snps, svs, [] ], fasta, fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam.bai', checkIfExists: true)
+                    ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("[ bam, bai, snps, [], [] ], fasta, fai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test.snap b/modules/nf-core/longphase/phase/tests/main.nf.test.snap
new file mode 100644
index 00000000..8a38c1ca
--- /dev/null
+++ b/modules/nf-core/longphase/phase/tests/main.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "[ bam, bai, snps, [], [] ], fasta, fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-22T12:14:04.269956432"
+    },
+    "[ bam, bai, snps, svs, [] ], fasta, fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-04T13:37:16.921910004"
+    },
+    "[ bam x2, bai x2, snps, svs, [] ], fasta, fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-04T13:37:23.41768963"
+    },
+    "[ bam, bai, snps, [], [] ], fasta, fai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8d8d82510dd1fbe01a91c575c472897f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-22T12:15:40.296227382"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/longphase/phase/tests/nextflow.config b/modules/nf-core/longphase/phase/tests/nextflow.config
new file mode 100644
index 00000000..317f040a
--- /dev/null
+++ b/modules/nf-core/longphase/phase/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'LONGPHASE_PHASE' {
+        ext.args = '--ont'
+    }
+}
diff --git a/modules/nf-core/longphase/phase/tests/tags.yml b/modules/nf-core/longphase/phase/tests/tags.yml
new file mode 100644
index 00000000..260a0d08
--- /dev/null
+++ b/modules/nf-core/longphase/phase/tests/tags.yml
@@ -0,0 +1,2 @@
+longphase/phase:
+  - "modules/nf-core/longphase/phase/**"
diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml
index 41e8fe9f..dc6476b7 100644
--- a/modules/nf-core/minimap2/align/environment.yml
+++ b/modules/nf-core/minimap2/align/environment.yml
@@ -1,9 +1,6 @@
-name: minimap2_align
-
 channels:
   - conda-forge
   - bioconda
-  - defaults
 
 dependencies:
   - bioconda::htslib=1.20
diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml
index 8996f881..a4cfc891 100644
--- a/modules/nf-core/minimap2/align/meta.yml
+++ b/modules/nf-core/minimap2/align/meta.yml
@@ -14,62 +14,77 @@ tools:
       homepage: https://github.com/lh3/minimap2
       documentation: https://github.com/lh3/minimap2#uguide
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FASTA or FASTQ files of size 1 and 2 for single-end
-        and paired-end data, respectively.
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test_ref']
-  - reference:
-      type: file
-      description: |
-        Reference database in FASTA format.
-  - bam_format:
-      type: boolean
-      description: Specify that output should be in BAM format
-  - bam_index_extension:
-      type: string
-      description: BAM alignment index extension (e.g. "bai")
-  - cigar_paf_format:
-      type: boolean
-      description: Specify that output CIGAR should be in PAF format
-  - cigar_bam:
-      type: boolean
-      description: |
-        Write CIGAR with >65535 ops at the CG tag. This is recommended when
-        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FASTA or FASTQ files of size 1 and 2 for single-end
+          and paired-end data, respectively.
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test_ref']
+    - reference:
+        type: file
+        description: |
+          Reference database in FASTA format.
+  - - bam_format:
+        type: boolean
+        description: Specify that output should be in BAM format
+  - - bam_index_extension:
+        type: string
+        description: BAM alignment index extension (e.g. "bai")
+  - - cigar_paf_format:
+        type: boolean
+        description: Specify that output CIGAR should be in PAF format
+  - - cigar_bam:
+        type: boolean
+        description: |
+          Write CIGAR with >65535 ops at the CG tag. This is recommended when
+          doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - paf:
-      type: file
-      description: Alignment in PAF format
-      pattern: "*.paf"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.paf":
+          type: file
+          description: Alignment in PAF format
+          pattern: "*.paf"
   - bam:
-      type: file
-      description: Alignment in BAM format
-      pattern: "*.bam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Alignment in BAM format
+          pattern: "*.bam"
   - index:
-      type: file
-      description: BAM alignment index
-      pattern: "*.bam.*"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam.${bam_index_extension}":
+          type: file
+          description: BAM alignment index
+          pattern: "*.bam.*"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@heuermh"
   - "@sofstam"
diff --git a/modules/nf-core/minimap2/index/environment.yml b/modules/nf-core/minimap2/index/environment.yml
index 8a912a12..d1c1b471 100644
--- a/modules/nf-core/minimap2/index/environment.yml
+++ b/modules/nf-core/minimap2/index/environment.yml
@@ -1,7 +1,5 @@
-name: minimap2_index
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::minimap2=2.28
diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml
index 1d29e3f2..57c80e29 100644
--- a/modules/nf-core/minimap2/index/meta.yml
+++ b/modules/nf-core/minimap2/index/meta.yml
@@ -11,30 +11,33 @@ tools:
       homepage: https://github.com/lh3/minimap2
       documentation: https://github.com/lh3/minimap2#uguide
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fasta:
-      type: file
-      description: |
-        Reference database in FASTA format.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: |
+          Reference database in FASTA format.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - index:
-      type: file
-      description: Minimap2 fasta index.
-      pattern: "*.mmi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.mmi":
+          type: file
+          description: Minimap2 fasta index.
+          pattern: "*.mmi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@yuukiiwa"
   - "@drpatelh"
diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml
index 95074539..1343a05b 100644
--- a/modules/nf-core/modkit/pileup/environment.yml
+++ b/modules/nf-core/modkit/pileup/environment.yml
@@ -1,7 +1,5 @@
-name: modkit_pileup
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - ont-modkit=0.3.0
diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml
index eb2875f4..2f274d0c 100644
--- a/modules/nf-core/modkit/pileup/meta.yml
+++ b/modules/nf-core/modkit/pileup/meta.yml
@@ -6,67 +6,83 @@ keywords:
   - long-read
 tools:
   - "modkit":
-      description: A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
+      description: A bioinformatics tool for working with modified bases in Oxford Nanopore
+        sequencing data
       homepage: https://github.com/nanoporetech/modkit
       documentation: https://github.com/nanoporetech/modkit
       tool_dev_url: https://github.com/nanoporetech/modkit
       licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test', single_end:false ]`
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM file
-      pattern: "*.{bam,cram}"
-  - bai:
-      type: file
-      description: Associated index file for BAM
-      pattern: "*.bai"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. `[ id:'hg38' ]`
-  - fasta:
-      type: file
-      description: Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering
-      pattern: "*.fasta"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing BED file information
-        e.g. `[ id:'regions' ]`
-  - bed:
-      type: file
-      description:
-        BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the
-        file
-      pattern: "*.bed"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM file
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: Associated index file for BAM
+        pattern: "*.bai"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'hg38' ]`
+    - fasta:
+        type: file
+        description: Reference sequence in FASTA format. Required for motif (e.g. CpG)
+          filtering
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing BED file information
+          e.g. `[ id:'regions' ]`
+    - bed:
+        type: file
+        description: BED file that will restrict threshold estimation and pileup results
+          to positions overlapping intervals in the file
+        pattern: "*.bed"
 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"
   - bed:
-      type: file
-      description: bedMethyl output file(s)
-      pattern: "*.bed"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.bed":
+          type: file
+          description: bedMethyl output file(s)
+          pattern: "*.bed"
   - bedgraph:
-      type: file
-      description: bedgraph output files
-      pattern: "*.bedgraph"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.bedgraph":
+          type: file
+          description: bedgraph output files
+          pattern: "*.bedgraph"
   - log:
-      type: file
-      description: File for debug logs to be written to
-      pattern: "*.log"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.log":
+          type: file
+          description: File for debug logs to be written to
+          pattern: "*.log"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@Michal-Babins"
   - "@fellen31"
diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml
index bcb9d64a..e9379873 100644
--- a/modules/nf-core/mosdepth/environment.yml
+++ b/modules/nf-core/mosdepth/environment.yml
@@ -1,8 +1,6 @@
-name: mosdepth
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   # renovate: datasource=conda depName=bioconda/mosdepth
   - mosdepth=0.3.8
diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml
index 9caaf2cd..dc783c90 100644
--- a/modules/nf-core/mosdepth/meta.yml
+++ b/modules/nf-core/mosdepth/meta.yml
@@ -12,91 +12,161 @@ tools:
       documentation: https://github.com/brentp/mosdepth
       doi: 10.1093/bioinformatics/btx699
       licence: ["MIT"]
+      identifier: biotools:mosdepth
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: Input BAM/CRAM file
-      pattern: "*.{bam,cram}"
-  - bai:
-      type: file
-      description: Index for BAM/CRAM file
-      pattern: "*.{bai,crai}"
-  - bed:
-      type: file
-      description: BED file with intersected intervals
-      pattern: "*.{bed}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing bed information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: Reference genome FASTA file
-      pattern: "*.{fa,fasta}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Input BAM/CRAM file
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: Index for BAM/CRAM file
+        pattern: "*.{bai,crai}"
+    - bed:
+        type: file
+        description: BED file with intersected intervals
+        pattern: "*.{bed}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing bed information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: Reference genome FASTA file
+        pattern: "*.{fa,fasta}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - global_txt:
-      type: file
-      description: Text file with global cumulative coverage distribution
-      pattern: "*.{global.dist.txt}"
-  - regions_txt:
-      type: file
-      description: Text file with region cumulative coverage distribution
-      pattern: "*.{region.dist.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.global.dist.txt":
+          type: file
+          description: Text file with global cumulative coverage distribution
+          pattern: "*.{global.dist.txt}"
   - summary_txt:
-      type: file
-      description: Text file with summary mean depths per chromosome and regions
-      pattern: "*.{summary.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.summary.txt":
+          type: file
+          description: Text file with summary mean depths per chromosome and regions
+          pattern: "*.{summary.txt}"
+  - regions_txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.region.dist.txt":
+          type: file
+          description: Text file with region cumulative coverage distribution
+          pattern: "*.{region.dist.txt}"
+  - per_base_d4:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.per-base.d4":
+          type: file
+          description: D4 file with per-base coverage
+          pattern: "*.{per-base.d4}"
   - per_base_bed:
-      type: file
-      description: BED file with per-base coverage
-      pattern: "*.{per-base.bed.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.per-base.bed.gz":
+          type: file
+          description: BED file with per-base coverage
+          pattern: "*.{per-base.bed.gz}"
   - per_base_csi:
-      type: file
-      description: Index file for BED file with per-base coverage
-      pattern: "*.{per-base.bed.gz.csi}"
-  - per_base_d4:
-      type: file
-      description: D4 file with per-base coverage
-      pattern: "*.{per-base.d4}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.per-base.bed.gz.csi":
+          type: file
+          description: Index file for BED file with per-base coverage
+          pattern: "*.{per-base.bed.gz.csi}"
   - regions_bed:
-      type: file
-      description: BED file with per-region coverage
-      pattern: "*.{regions.bed.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.regions.bed.gz":
+          type: file
+          description: BED file with per-region coverage
+          pattern: "*.{regions.bed.gz}"
   - regions_csi:
-      type: file
-      description: Index file for BED file with per-region coverage
-      pattern: "*.{regions.bed.gz.csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.regions.bed.gz.csi":
+          type: file
+          description: Index file for BED file with per-region coverage
+          pattern: "*.{regions.bed.gz.csi}"
   - quantized_bed:
-      type: file
-      description: BED file with binned coverage
-      pattern: "*.{quantized.bed.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.quantized.bed.gz":
+          type: file
+          description: BED file with binned coverage
+          pattern: "*.{quantized.bed.gz}"
   - quantized_csi:
-      type: file
-      description: Index file for BED file with binned coverage
-      pattern: "*.{quantized.bed.gz.csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.quantized.bed.gz.csi":
+          type: file
+          description: Index file for BED file with binned coverage
+          pattern: "*.{quantized.bed.gz.csi}"
   - thresholds_bed:
-      type: file
-      description: BED file with the number of bases in each region that are covered at or above each threshold
-      pattern: "*.{thresholds.bed.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.thresholds.bed.gz":
+          type: file
+          description: BED file with the number of bases in each region that are covered
+            at or above each threshold
+          pattern: "*.{thresholds.bed.gz}"
   - thresholds_csi:
-      type: file
-      description: Index file for BED file with threshold coverage
-      pattern: "*.{thresholds.bed.gz.csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.thresholds.bed.gz.csi":
+          type: file
+          description: Index file for BED file with threshold coverage
+          pattern: "*.{thresholds.bed.gz.csi}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test
index 21eebc1f..0b3c860d 100644
--- a/modules/nf-core/mosdepth/tests/main.nf.test
+++ b/modules/nf-core/mosdepth/tests/main.nf.test
@@ -15,8 +15,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
                 ]
                 input[1] = [[],[]]
@@ -40,9 +40,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
                 """
@@ -65,13 +65,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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.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] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -93,13 +93,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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']['genome']['genome_bed'], checkIfExists: true)
+                    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),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -122,8 +122,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
                 ]
                 input[1] = [[],[]]
@@ -148,8 +148,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
                     []
                 ]
                 input[1] = [[],[]]
@@ -174,9 +174,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
                 """
@@ -200,9 +200,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
                 """
@@ -225,9 +225,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [[],[]]
                 """
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb67..6f5b867b 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352f..cc0643e1 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     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}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
@@ -44,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc35..b16c1879 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242e..33316a7d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 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] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd802..2fcbb5ff 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 00000000..c537a6a3
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml
index 3c9f5526..3722ded7 100644
--- a/modules/nf-core/paraphase/environment.yml
+++ b/modules/nf-core/paraphase/environment.yml
@@ -1,9 +1,6 @@
-name: paraphase
-
 channels:
   - conda-forge
   - bioconda
-  - defaults
 
 dependencies:
   - bioconda::minimap2=2.28
diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf
index ddaa33ec..8474427e 100644
--- a/modules/nf-core/paraphase/main.nf
+++ b/modules/nf-core/paraphase/main.nf
@@ -14,17 +14,20 @@ process PARAPHASE {
     tuple val(meta3), path(config)
 
     output:
-    tuple val(meta), path("*.paraphase.json")              , emit: json
-    tuple val(meta), path("*.paraphase.bam")               , emit: bam
-    tuple val(meta), path("*.paraphase.bam.bai")           , emit: bai
-    tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf"), emit: vcf, optional: true
-    path "versions.yml"                                    , emit: versions
+    tuple val(meta), path("*.paraphase.json")                           , emit: json
+    tuple val(meta), path("*.paraphase.bam")                            , emit: bam
+    tuple val(meta), path("*.paraphase.bam.bai")                        , emit: bai
+    tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz")          , emit: vcf      , optional: true
+    tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true
+    path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def config_file = config ? "--config $config" : ""
     """
@@ -37,6 +40,18 @@ process PARAPHASE {
         $config_file \\
         --out .
 
+    for vcf in ${prefix}_paraphase_vcfs/*.vcf;
+    do
+        bgzip \\
+            $args2 \\
+            --threads $task.cpus \\
+            \$vcf;
+        tabix \\
+            $args3 \\
+            --threads $task.cpus \\
+            \$vcf.gz;
+    done
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         minimap2: \$(minimap2 --version 2>&1)
@@ -46,15 +61,18 @@ process PARAPHASE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args3 = task.ext.args3 ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+
+    def index = args3.contains('--csi') ? 'csi' : 'tbi'
     """
     mkdir ${prefix}_paraphase_vcfs
 
     touch ${prefix}.paraphase.json
     touch ${prefix}.paraphase.bam
     touch ${prefix}.paraphase.bam.bai
-    touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf
+    echo '' | gzip > ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz
+    touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz.${index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml
index 4dae0dd8..50c3c9e0 100644
--- a/modules/nf-core/paraphase/meta.yml
+++ b/modules/nf-core/paraphase/meta.yml
@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "paraphase"
 description: "HiFi-based caller for highly homologous genes"
@@ -14,69 +13,96 @@ tools:
       tool_dev_url: "https://github.com/PacificBiosciences/paraphase"
       doi: "10.1016/j.ajhg.2023.01.001"
       licence: ["BSD-3-clause-Clear"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:true ]`
-
-  - bam:
-      type: file
-      description: Sorted BAM file
-      pattern: "*.bam"
-
-  - bai:
-      type: file
-      description: Index of BAM file
-      pattern: "*.bai"
-
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: The reference fasta file
-      pattern: "*.fasta"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing config information
-        e.g. [ id:'config' ]
-  - config:
-      type: file
-      description: Config file
-      pattern: "*.yaml"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:true ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: Index of BAM file
+        pattern: "*.bai"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing config information
+          e.g. [ id:'config' ]
+    - config:
+        type: file
+        description: Config file
+        pattern: "*.yaml"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:true ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  - json:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:true ]`
+      - "*.paraphase.json":
+          type: file
+          description: Summary of haplotype and variant calls
+          pattern: "*.paraphase.json"
   - bam:
-      type: file
-      description: (re)aligned BAM file
-      pattern: "*.paraphase.bam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:true ]`
+      - "*.paraphase.bam":
+          type: file
+          description: (re)aligned BAM file
+          pattern: "*.paraphase.bam"
   - bai:
-      type: file
-      description: Index of (re)aligned BAM file
-      pattern: "*.paraphase.bam.bai"
-  - json:
-      type: file
-      description: Summary of haplotype and variant calls
-      pattern: "*.paraphase.json"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:true ]`
+      - "*.paraphase.bam.bai":
+          type: file
+          description: Index of (re)aligned BAM file
+          pattern: "*.paraphase.bam.bai"
   - vcf:
-      type: file
-      description: VCF file(s) per gene
-      pattern: "*.vcf"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:true ]`
+      - ${prefix}_paraphase_vcfs/*.vcf.gz:
+          type: file
+          description: compressed VCF file(s) per gene
+          pattern: "*.vcf.gz"
+  - vcf_index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:true ]`
+      - ${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}:
+          type: file
+          description: compressed VCF file index
+          pattern: "*.vcf.gz.{tbi,csi}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@fellen31"
 maintainers:
diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test
index ff35588f..e34d6699 100644
--- a/modules/nf-core/paraphase/tests/main.nf.test
+++ b/modules/nf-core/paraphase/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process PARAPHASE"
     script "../main.nf"
     process "PARAPHASE"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -25,6 +24,9 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ bam, bai ], []") {
+
+        config "./nextflow.config"
+
         when {
             process {
                 """
@@ -45,16 +47,16 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") },
                 { assert snapshot(
                     file(process.out.json.get(0).get(1)).readLines()[0..39],
-                    process.out.versions,
-                    file(process.out.vcf.get(0).get(1)).readLines()[0..962],
-                    process.out.bam ==~ "test.paraphase.bam",
-                    process.out.bai ==~ "test.paraphase.bam.bai",
+                    path(process.out.vcf.get(0).get(1)).linesGzip[10],
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    file(process.out.bai.get(0).get(1)).name,
+                    file(process.out.vcf_index.get(0).get(1)).name,
+                    process.out.versions
                     ).match()
-                },
-                { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" },
-                { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" },
+                }
             )
         }
 
@@ -62,6 +64,46 @@ nextflow_process {
 
     test("homo_sapiens - [ bam, bai ], config") {
 
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                ]
+                input[1] = TABIX_BGZIP.out.output
+                input[2] = [
+                    [ id:'test_config' ],
+                    file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    file(process.out.json.get(0).get(1)).readLines()[0..39],
+                    path(process.out.vcf.get(0).get(1)).linesGzip[10],
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    file(process.out.bai.get(0).get(1)).name,
+                    file(process.out.vcf_index.get(0).get(1)).name,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("homo_sapiens - [ bam, bai ], config - csi_index") {
+
+        config "./nextflow.csi_index.config"
+
         when {
             process {
                 """
@@ -82,16 +124,16 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.vcf_index.get(0).get(1).endsWith("csi") },
                 { assert snapshot(
                     file(process.out.json.get(0).get(1)).readLines()[0..39],
-                    process.out.versions,
-                    file(process.out.vcf.get(0).get(1)).readLines()[0..962],
-                    process.out.bam ==~ "test.paraphase.bam",
-                    process.out.bai ==~ "test.paraphase.bam.bai",
+                    path(process.out.vcf.get(0).get(1)).linesGzip[10],
+                    bam(process.out.bam.get(0).get(1)).getReadsMD5(),
+                    file(process.out.bai.get(0).get(1)).name,
+                    file(process.out.vcf_index.get(0).get(1)).name,
+                    process.out.versions
                     ).match()
-                },
-                { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" },
-                { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" },
+                }
             )
         }
     }
@@ -99,6 +141,7 @@ nextflow_process {
     test("homo_sapiens - [ bam, bai ], [] - stub") {
 
         options "-stub"
+        config "./nextflow.config"
 
         when {
             process {
@@ -128,6 +171,37 @@ nextflow_process {
     test("homo_sapiens - [ bam, bai ], config - stub") {
 
         options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                ]
+                input[1] = TABIX_BGZIP.out.output
+                input[2] = [
+                    [ id:'test_config' ],
+                    file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [ bam, bai ], config - stub - csi_index") {
+
+        options "-stub"
+        config "./nextflow.csi_index.config"
 
         when {
             process {
diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap
index 32242c1c..b80a3443 100644
--- a/modules/nf-core/paraphase/tests/main.nf.test.snap
+++ b/modules/nf-core/paraphase/tests/main.nf.test.snap
@@ -43,982 +43,19 @@
                 "        \"unique_supporting_reads\": {",
                 "            \"12222212222111211221\": ["
             ],
+            "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5",
+            "add24d02bf7f37b3ca30771c44ab4ee2",
+            "test.paraphase.bam.bai",
+            "test_PRODH.vcf.gz.tbi",
             [
                 "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
-            ],
-            [
-                "##fileformat=VCFv4.2",
-                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
-                "##INFO=<ID=HPBOUND,Number=.,Type=String,Description=\"Boundary coordinates of the phased haplotype\">",
-                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype per haplotype\">",
-                "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Depth per haplotype\">",
-                "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Read depth for REF and ALT per haplotype\">",
-                "##contig=<ID=chr22,length=50818468>",
-                "##paraphase_version=3.1.1",
-                "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --out .",
-                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2",
-                "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5",
-                "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6",
-                "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3",
-                "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1",
-                "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7",
-                "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7",
-                "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3",
-                "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4",
-                "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912326\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912327\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912328\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912329\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912330\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912331\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912332\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912333\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912334\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912335\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912336\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912337\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912338\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912339\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912340\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912341\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912342\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912343\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912344\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912345\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912346\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912347\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:4:0,3",
-                "chr22\t18912348\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912349\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912350\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912351\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912352\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2",
-                "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7",
-                "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4",
-                "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912407\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912408\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912409\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912410\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912411\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912412\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912413\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912414\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912415\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912416\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912417\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912418\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912419\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912420\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912421\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912422\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912423\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912424\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912425\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912426\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912427\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912428\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912429\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912430\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912431\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912432\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912433\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912434\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912435\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912436\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912437\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912438\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912439\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912440\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912441\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912442\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912443\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912444\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912445\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912446\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912447\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912448\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912449\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912450\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912451\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912452\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912453\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912454\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912455\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912456\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912457\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912458\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3",
-                "chr22\t18912459\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912460\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912461\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912462\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912463\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912464\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912465\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912466\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912467\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912468\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912469\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912497\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912498\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912499\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912500\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912501\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912502\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912503\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912504\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912505\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912506\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2",
-                "chr22\t18912507\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912508\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912509\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912510\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912511\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912512\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912513\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912514\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912515\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912516\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912517\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912518\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912519\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912520\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912521\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912522\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912523\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912524\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912525\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912526\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912527\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912528\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,4",
-                "chr22\t18912529\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2",
-                "chr22\t18912530\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912531\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912532\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912533\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912534\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912535\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912536\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912537\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912538\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912539\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912540\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912541\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912542\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912543\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912544\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912545\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912546\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912547\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912548\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912549\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912550\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912551\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912552\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912553\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912554\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912555\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912556\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912557\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912558\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,5",
-                "chr22\t18912559\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t.:4:0,2",
-                "chr22\t18912560\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912561\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912562\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912563\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912564\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912565\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912566\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912567\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912568\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4",
-                "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3",
-                "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4",
-                "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912596\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912597\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912598\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912599\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912600\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912601\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912602\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912603\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912604\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912605\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912606\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912607\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912608\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912609\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912610\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912611\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912612\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912613\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6",
-                "chr22\t18912614\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912615\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912616\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:2:0,2",
-                "chr22\t18912617\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912618\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912619\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912620\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:6:0,6",
-                "chr22\t18912621\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912622\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912623\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912624\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912625\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912626\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912627\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912628\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912629\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912630\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912631\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912632\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912633\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912634\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912635\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912636\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912637\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912638\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912639\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912640\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912641\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912642\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912643\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912644\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912645\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912646\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912647\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912648\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912649\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912650\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912651\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912652\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912653\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912654\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912655\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912656\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912657\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912658\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912659\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912660\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,6",
-                "chr22\t18912661\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2",
-                "chr22\t18912662\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912663\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912664\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912665\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912666\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912667\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912668\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912669\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912670\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912671\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912672\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912673\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912674\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912675\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912676\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912686\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912687\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912688\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912689\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912690\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912691\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912692\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912693\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18912694\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912695\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6",
-                "chr22\t18912696\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912697\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912698\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912699\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912700\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912701\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912702\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912703\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912704\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912705\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912706\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912707\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912708\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912709\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912710\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912711\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912712\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912713\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912714\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,6",
-                "chr22\t18912715\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912716\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912717\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912718\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912719\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912720\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912721\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912722\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912723\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912724\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912725\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4",
-                "chr22\t18912726\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912727\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912728\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912729\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18912730\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,3",
-                "chr22\t18912731\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912732\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912733\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912734\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912735\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912736\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912737\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912738\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912739\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912740\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912741\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912742\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912743\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912744\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912745\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912746\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912747\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912748\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912749\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912750\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912751\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912752\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912753\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912754\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912755\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912756\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912757\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912758\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912759\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912760\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912761\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912762\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912763\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:4:0,4",
-                "chr22\t18912764\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912765\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912766\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3",
-                "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7",
-                "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912785\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912786\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912787\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912788\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912789\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912790\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912791\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912792\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912793\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912803\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912804\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912805\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912806\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912807\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912808\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912809\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912810\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912811\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912812\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912813\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912814\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18912815\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t1:4:0,4",
-                "chr22\t18912816\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912817\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912818\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912819\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912820\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912821\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912822\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912823\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912824\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912825\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912826\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912827\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912828\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912829\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912830\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912831\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912832\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912833\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912834\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,3",
-                "chr22\t18912835\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912836\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912837\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912838\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7",
-                "chr22\t18912839\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912840\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,2",
-                "chr22\t18912841\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912842\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912843\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912844\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912845\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912846\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912847\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3",
-                "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4",
-                "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2",
-                "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912911\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912912\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912913\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912914\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912915\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912916\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912917\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7",
-                "chr22\t18912918\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t.:2:0,2",
-                "chr22\t18912919\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912920\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912921\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912922\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6",
-                "chr22\t18912923\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912924\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912925\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912926\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912927\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912928\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912929\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18912930\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,3",
-                "chr22\t18912931\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912932\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912933\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912934\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912935\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912936\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912937\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912938\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912939\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912940\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912941\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912942\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912943\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912944\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912945\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912946\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6",
-                "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4",
-                "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3",
-                "chr22\t18913010\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913011\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913012\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913013\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913014\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913015\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913016\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913017\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913018\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913019\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913020\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913021\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913022\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913023\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913024\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913025\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913026\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913027\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913028\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18913029\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18913030\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913031\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913032\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913033\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18913034\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913035\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913036\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2",
-                "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913100\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3",
-                "chr22\t18913101\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913102\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913103\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5",
-                "chr22\t18913104\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5",
-                "chr22\t18913105\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913106\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913107\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913108\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913109\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913110\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913111\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913112\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913113\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913114\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913115\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913116\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913117\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913118\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913119\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913120\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913121\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913122\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913123\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913124\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913125\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913126\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913127\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913128\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913129\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913130\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913131\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913132\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6",
-                "chr22\t18913133\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:3:0,2",
-                "chr22\t18913134\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913135\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913136\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913137\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913138\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,5",
-                "chr22\t18913139\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,1",
-                "chr22\t18913140\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913141\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913142\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913143\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913144\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913154\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913155\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913156\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913157\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913158\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:2:0,2",
-                "chr22\t18913159\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913160\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18913161\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913162\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913199\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913200\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913201\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913202\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913203\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18913204\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18913205\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913206\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913207\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18913208\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913209\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913210\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913211\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913212\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913213\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913214\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913215\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913216\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5"
-            ],
-            false,
-            false
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-29T15:14:21.054789211"
+        "timestamp": "2024-09-06T06:20:55.135067843"
     },
     "homo_sapiens - [ bam, bai ], config - stub": {
         "content": [
@@ -1056,10 +93,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
                 ],
                 "bai": [
@@ -1095,7 +141,16 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcf_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -1105,9 +160,67 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-29T17:44:03.275093922"
+        "timestamp": "2024-09-03T12:04:30.019868621"
+    },
+    "homo_sapiens - [ bam, bai ], config - csi_index": {
+        "content": [
+            [
+                "{",
+                "    \"PRODH\": {",
+                "        \"total_cn\": 2,",
+                "        \"gene_cn\": null,",
+                "        \"final_haplotypes\": {",
+                "            \"12222212222111211221\": \"PRODH_hap1\",",
+                "            \"21111121111222122112\": \"PRODH_hap2\"",
+                "        },",
+                "        \"two_copy_haplotypes\": [],",
+                "        \"alleles_final\": [],",
+                "        \"hap_links\": {},",
+                "        \"highest_total_cn\": 2,",
+                "        \"assembled_haplotypes\": [",
+                "            \"12222212222111211221\",",
+                "            \"21111121111222122112\"",
+                "        ],",
+                "        \"sites_for_phasing\": [",
+                "            \"18913237_G_A\",",
+                "            \"18917224_G_A\",",
+                "            \"18917246_A_C\",",
+                "            \"18917262_G_A\",",
+                "            \"18917266_T_C\",",
+                "            \"18917362_C_A\",",
+                "            \"18918010_C_T\",",
+                "            \"18918465_G_A\",",
+                "            \"18918847_T_C\",",
+                "            \"18919892_G_T\",",
+                "            \"18920342_G_A\",",
+                "            \"18920484_C_T\",",
+                "            \"18921128_C_T\",",
+                "            \"18921213_T_C\",",
+                "            \"18921638_T_G\",",
+                "            \"18921763_T_C\",",
+                "            \"18922744_C_T\",",
+                "            \"18923032_C_T\",",
+                "            \"18923315_T_G\",",
+                "            \"18923644_G_A\"",
+                "        ],",
+                "        \"unique_supporting_reads\": {",
+                "            \"12222212222111211221\": ["
+            ],
+            "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5",
+            "add24d02bf7f37b3ca30771c44ab4ee2",
+            "test.paraphase.bam.bai",
+            "test_PRODH.vcf.gz.csi",
+            [
+                "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T06:24:48.142490096"
     },
     "homo_sapiens - [ bam, bai ], [] - stub": {
         "content": [
@@ -1145,10 +258,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
                 ],
                 "bai": [
@@ -1184,7 +306,16 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcf_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -1194,9 +325,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-29T17:43:56.008820548"
+        "timestamp": "2024-09-03T12:04:14.370756094"
     },
     "homo_sapiens - [ bam, bai ], config": {
         "content": [
@@ -1242,981 +373,125 @@
                 "        \"unique_supporting_reads\": {",
                 "            \"12222212222111211221\": ["
             ],
+            "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5",
+            "add24d02bf7f37b3ca30771c44ab4ee2",
+            "test.paraphase.bam.bai",
+            "test_PRODH.vcf.gz.tbi",
             [
                 "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
-            ],
-            [
-                "##fileformat=VCFv4.2",
-                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
-                "##INFO=<ID=HPBOUND,Number=.,Type=String,Description=\"Boundary coordinates of the phased haplotype\">",
-                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype per haplotype\">",
-                "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Depth per haplotype\">",
-                "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Read depth for REF and ALT per haplotype\">",
-                "##contig=<ID=chr22,length=50818468>",
-                "##paraphase_version=3.1.1",
-                "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --config paraphase_config.yaml --out .",
-                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2",
-                "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5",
-                "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6",
-                "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3",
-                "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1",
-                "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7",
-                "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7",
-                "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3",
-                "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4",
-                "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912326\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912327\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912328\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912329\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912330\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912331\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912332\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912333\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912334\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912335\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912336\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912337\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912338\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912339\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912340\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912341\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912342\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912343\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912344\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912345\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912346\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912347\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:4:0,3",
-                "chr22\t18912348\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912349\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912350\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912351\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912352\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2",
-                "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7",
-                "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4",
-                "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912407\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912408\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912409\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912410\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912411\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912412\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912413\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912414\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912415\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912416\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912417\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912418\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912419\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912420\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912421\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912422\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912423\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912424\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912425\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912426\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912427\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912428\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912429\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912430\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912431\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912432\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912433\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912434\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912435\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912436\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912437\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912438\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912439\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912440\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912441\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912442\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912443\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912444\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912445\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912446\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912447\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912448\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912449\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912450\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912451\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912452\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912453\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912454\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912455\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912456\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912457\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912458\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3",
-                "chr22\t18912459\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912460\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912461\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912462\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912463\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912464\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912465\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912466\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912467\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912468\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912469\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912497\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912498\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912499\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912500\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912501\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912502\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912503\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912504\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912505\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912506\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2",
-                "chr22\t18912507\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912508\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912509\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912510\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912511\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912512\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912513\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912514\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912515\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912516\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912517\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912518\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912519\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912520\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912521\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912522\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912523\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912524\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912525\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912526\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912527\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912528\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,4",
-                "chr22\t18912529\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2",
-                "chr22\t18912530\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912531\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912532\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912533\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912534\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912535\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912536\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912537\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912538\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912539\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912540\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912541\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912542\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912543\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912544\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912545\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912546\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912547\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912548\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912549\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912550\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912551\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912552\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912553\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912554\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912555\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912556\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912557\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912558\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,5",
-                "chr22\t18912559\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t.:4:0,2",
-                "chr22\t18912560\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912561\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912562\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912563\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912564\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912565\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912566\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912567\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912568\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4",
-                "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3",
-                "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4",
-                "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912596\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912597\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912598\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912599\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912600\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912601\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912602\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912603\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912604\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912605\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912606\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912607\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912608\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912609\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912610\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912611\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912612\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912613\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6",
-                "chr22\t18912614\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912615\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912616\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:2:0,2",
-                "chr22\t18912617\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912618\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912619\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912620\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:6:0,6",
-                "chr22\t18912621\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912622\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912623\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912624\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912625\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912626\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912627\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912628\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912629\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912630\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912631\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912632\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912633\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912634\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912635\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912636\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912637\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912638\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912639\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912640\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912641\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912642\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912643\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912644\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912645\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912646\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912647\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912648\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912649\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912650\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912651\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912652\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912653\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3",
-                "chr22\t18912654\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912655\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912656\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912657\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912658\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912659\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912660\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,6",
-                "chr22\t18912661\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2",
-                "chr22\t18912662\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912663\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912664\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912665\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912666\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912667\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912668\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912669\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912670\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912671\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912672\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912673\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912674\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912675\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912676\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912686\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912687\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912688\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912689\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912690\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912691\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912692\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912693\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18912694\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912695\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6",
-                "chr22\t18912696\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912697\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912698\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912699\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912700\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912701\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912702\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912703\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912704\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912705\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912706\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912707\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912708\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912709\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912710\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912711\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912712\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912713\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912714\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,6",
-                "chr22\t18912715\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912716\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912717\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912718\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912719\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912720\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912721\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912722\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912723\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912724\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912725\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4",
-                "chr22\t18912726\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912727\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912728\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912729\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18912730\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,3",
-                "chr22\t18912731\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912732\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912733\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912734\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912735\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912736\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912737\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912738\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912739\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912740\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912741\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912742\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912743\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912744\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912745\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912746\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912747\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912748\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912749\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912750\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912751\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912752\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912753\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912754\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912755\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912756\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912757\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912758\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912759\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912760\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912761\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912762\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912763\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:4:0,4",
-                "chr22\t18912764\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912765\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912766\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3",
-                "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7",
-                "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912785\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912786\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912787\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912788\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912789\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912790\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912791\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912792\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912793\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912803\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912804\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912805\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912806\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912807\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912808\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912809\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912810\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912811\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912812\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912813\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912814\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18912815\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t1:4:0,4",
-                "chr22\t18912816\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912817\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912818\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912819\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912820\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912821\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912822\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912823\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912824\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912825\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912826\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912827\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912828\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912829\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912830\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912831\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912832\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912833\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912834\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,3",
-                "chr22\t18912835\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912836\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912837\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912838\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7",
-                "chr22\t18912839\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912840\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,2",
-                "chr22\t18912841\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912842\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912843\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912844\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912845\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912846\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5",
-                "chr22\t18912847\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3",
-                "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6",
-                "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4",
-                "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4",
-                "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5",
-                "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2",
-                "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912911\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912912\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912913\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912914\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912915\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912916\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912917\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7",
-                "chr22\t18912918\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t.:2:0,2",
-                "chr22\t18912919\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912920\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912921\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912922\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6",
-                "chr22\t18912923\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912924\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912925\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912926\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912927\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18912928\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912929\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18912930\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,3",
-                "chr22\t18912931\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912932\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6",
-                "chr22\t18912933\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912934\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912935\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912936\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912937\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18912938\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18912939\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912940\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912941\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912942\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912943\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912944\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912945\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912946\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6",
-                "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4",
-                "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4",
-                "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3",
-                "chr22\t18913010\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913011\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913012\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913013\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913014\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913015\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913016\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913017\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913018\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913019\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913020\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913021\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913022\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913023\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913024\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913025\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913026\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913027\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913028\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18913029\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18913030\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913031\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913032\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913033\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4",
-                "chr22\t18913034\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913035\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913036\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7",
-                "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2",
-                "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6",
-                "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913100\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3",
-                "chr22\t18913101\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913102\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913103\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5",
-                "chr22\t18913104\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5",
-                "chr22\t18913105\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913106\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913107\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913108\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913109\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913110\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913111\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913112\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913113\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913114\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913115\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913116\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913117\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913118\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5",
-                "chr22\t18913119\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913120\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913121\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913122\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913123\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913124\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913125\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913126\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913127\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913128\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913129\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913130\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913131\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913132\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6",
-                "chr22\t18913133\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:3:0,2",
-                "chr22\t18913134\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913135\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913136\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913137\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913138\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,5",
-                "chr22\t18913139\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,1",
-                "chr22\t18913140\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913141\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913142\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913143\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913144\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913154\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913155\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913156\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913157\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913158\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:2:0,2",
-                "chr22\t18913159\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913160\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7",
-                "chr22\t18913161\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913162\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5",
-                "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4",
-                "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6",
-                "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913199\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913200\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913201\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6",
-                "chr22\t18913202\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913203\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6",
-                "chr22\t18913204\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5",
-                "chr22\t18913205\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913206\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913207\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3",
-                "chr22\t18913208\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913209\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913210\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913211\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5",
-                "chr22\t18913212\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913213\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913214\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913215\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913216\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6",
-                "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6",
-                "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5",
-                "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7",
-                "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7",
-                "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7",
-                "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5"
-            ],
-            false,
-            false
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T06:24:34.443854854"
+    },
+    "homo_sapiens - [ bam, bai ], config - stub - csi_index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcf_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-29T15:14:33.451355236"
+        "timestamp": "2024-09-03T12:10:23.256066977"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/paraphase/tests/nextflow.csi_index.config b/modules/nf-core/paraphase/tests/nextflow.csi_index.config
new file mode 100644
index 00000000..df8ee6c3
--- /dev/null
+++ b/modules/nf-core/paraphase/tests/nextflow.csi_index.config
@@ -0,0 +1,6 @@
+process {
+    withName: 'PARAPHASE' {
+        ext.args = '--gene PRODH'
+        ext.args3 = '--csi'
+    }
+}
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index f8450fa5..62054fc9 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -1,10 +1,8 @@
-name: samtools_faidx
-
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
-
 dependencies:
-  - bioconda::htslib=1.20
-  - bioconda::samtools=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index bdcdbc95..28c0a81c 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:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index f3c25de2..6721b2cb 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -14,47 +14,62 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa,fasta}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test' ]
-  - fai:
-      type: file
-      description: FASTA index file
-      pattern: "*.{fai}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.{fai}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - fa:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{fa,fasta}":
+          type: file
+          description: FASTA file
+          pattern: "*.{fa}"
   - fai:
-      type: file
-      description: FASTA index file
-      pattern: "*.{fai}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fai":
+          type: file
+          description: FASTA index file
+          pattern: "*.{fai}"
   - gzi:
-      type: file
-      description: Optional gzip index file for compressed inputs
-      pattern: "*.gzi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gzi":
+          type: file
+          description: Optional gzip index file for compressed inputs
+          pattern: "*.gzi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
index 3223b72b..1bbb3ec2 100644
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ],
                 "fa": [
                     
@@ -36,15 +36,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:14.779784761"
+        "timestamp": "2024-09-16T07:57:47.450887871"
     },
     "test_samtools_faidx_bgzip": {
         "content": [
@@ -71,7 +71,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ],
                 "fa": [
                     
@@ -95,15 +95,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:20.256633877"
+        "timestamp": "2024-09-16T07:58:04.804905659"
     },
     "test_samtools_faidx_fasta": {
         "content": [
@@ -124,7 +124,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ],
                 "fa": [
                     [
@@ -142,15 +142,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:25.632577273"
+        "timestamp": "2024-09-16T07:58:23.831268154"
     },
     "test_samtools_faidx_stub_fasta": {
         "content": [
@@ -171,7 +171,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ],
                 "fa": [
                     [
@@ -189,15 +189,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:31.058424849"
+        "timestamp": "2024-09-16T07:58:35.600243706"
     },
     "test_samtools_faidx_stub_fai": {
         "content": [
@@ -218,7 +218,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ],
                 "fa": [
                     
@@ -236,14 +236,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
+                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:36.479929617"
+        "timestamp": "2024-09-16T07:58:54.705460167"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml
index 4455904e..62054fc9 100644
--- a/modules/nf-core/samtools/fastq/environment.yml
+++ b/modules/nf-core/samtools/fastq/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_fastq
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf
index 6796c02b..136744d5 100644
--- a/modules/nf-core/samtools/fastq/main.nf
+++ b/modules/nf-core/samtools/fastq/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_FASTQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/fastq/meta.yml b/modules/nf-core/samtools/fastq/meta.yml
index c4002a45..c15a0b6f 100644
--- a/modules/nf-core/samtools/fastq/meta.yml
+++ b/modules/nf-core/samtools/fastq/meta.yml
@@ -15,45 +15,69 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - interleave:
-      type: boolean
-      description: Set true for interleaved fastq file
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+  - - interleave:
+        type: boolean
+        description: Set true for interleaved fastq file
 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"
   - fastq:
-      type: file
-      description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
-      pattern: "*_{1,2}.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_{1,2}.fastq.gz":
+          type: file
+          description: Compressed FASTQ file(s) with reads with either the READ1 or READ2
+            flag set in separate files.
+          pattern: "*_{1,2}.fastq.gz"
   - interleaved:
-      type: file
-      description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
-      pattern: "*_interleaved.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_interleaved.fastq":
+          type: file
+          description: Compressed FASTQ file with reads with either the READ1 or READ2
+            flag set in a combined file. Needs collated input file.
+          pattern: "*_interleaved.fastq.gz"
   - singleton:
-      type: file
-      description: Compressed FASTQ file with singleton reads
-      pattern: "*_singleton.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_singleton.fastq.gz":
+          type: file
+          description: Compressed FASTQ file with singleton reads
+          pattern: "*_singleton.fastq.gz"
   - other:
-      type: file
-      description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
-      pattern: "*_other.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_other.fastq.gz":
+          type: file
+          description: Compressed FASTQ file with reads with either both READ1 and READ2
+            flags set or unset
+          pattern: "*_other.fastq.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@priyanka-surana"
   - "@suzannejin"
diff --git a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap
index 1ba09d3a..10e5cd3d 100644
--- a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap
@@ -93,26 +93,26 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1"
+                "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:40.362380302"
+        "timestamp": "2024-09-16T08:00:41.44921616"
     },
     "bam_verinterleave_sions": {
         "content": [
             [
-                "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1"
+                "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:45.632731997"
+        "timestamp": "2024-09-16T08:00:56.47781168"
     },
     "bam_singleton": {
         "content": [
diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml
index 38f1ebab..62054fc9 100644
--- a/modules/nf-core/samtools/import/environment.yml
+++ b/modules/nf-core/samtools/import/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_import
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/import/main.nf b/modules/nf-core/samtools/import/main.nf
index 954a8052..e0a51c03 100644
--- a/modules/nf-core/samtools/import/main.nf
+++ b/modules/nf-core/samtools/import/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_IMPORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0':
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0':
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/samtools/import/meta.yml b/modules/nf-core/samtools/import/meta.yml
index 9002e092..5c98b8be 100644
--- a/modules/nf-core/samtools/import/meta.yml
+++ b/modules/nf-core/samtools/import/meta.yml
@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "samtools_import"
 description: converts FASTQ files to unmapped SAM/BAM/CRAM
@@ -18,38 +17,53 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test', single_end:false ]`
-  - reads:
-      type: file
-      description: fastq data to be converted to SAM/BAM/CRAM
-      pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - reads:
+        type: file
+        description: fastq data to be converted to SAM/BAM/CRAM
+        pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
 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"
   - sam:
-      type: file
-      description: SAM file
-      pattern: "*.sam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.sam":
+          type: file
+          description: SAM file
+          pattern: "*.sam"
   - bam:
-      type: file
-      description: Unaligned BAM file
-      pattern: "*.bam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.bam":
+          type: file
+          description: Unaligned BAM file
+          pattern: "*.bam"
   - cram:
-      type: file
-      description: Unaligned CRAM file
-      pattern: "*.cram"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.cram":
+          type: file
+          description: Unaligned CRAM file
+          pattern: "*.cram"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@matthdsm"
 maintainers:
diff --git a/modules/nf-core/samtools/import/tests/main.nf.test b/modules/nf-core/samtools/import/tests/main.nf.test
index d029ca70..9c7ce5d9 100644
--- a/modules/nf-core/samtools/import/tests/main.nf.test
+++ b/modules/nf-core/samtools/import/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 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)
                 ])
                 """
             }
@@ -42,8 +42,8 @@ nextflow_process {
                 """
                 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)
                 ])
                 """
             }
@@ -67,7 +67,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
                 ])
                 """
             }
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
index 260d516b..62054fc9 100644
--- a/modules/nf-core/samtools/index/environment.yml
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_index
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index e002585b..31175610 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:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index 01a4ee03..db8df0d5 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -15,38 +15,52 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 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}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: input file
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bai:
-      type: file
-      description: BAM/CRAM/SAM index file
-      pattern: "*.{bai,crai,sai}"
-  - crai:
-      type: file
-      description: BAM/CRAM/SAM index file
-      pattern: "*.{bai,crai,sai}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bai":
+          type: file
+          description: BAM/CRAM/SAM index file
+          pattern: "*.{bai,crai,sai}"
   - csi:
-      type: file
-      description: CSI index file
-      pattern: "*.{csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: CSI index file
+          pattern: "*.{csi}"
+  - crai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: BAM/CRAM/SAM index file
+          pattern: "*.{bai,crai,sai}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
index 799d199c..72d65e81 100644
--- a/modules/nf-core/samtools/index/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ],
                 "bai": [
                     
@@ -36,15 +36,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:51:53.9057"
+        "timestamp": "2024-09-16T08:21:25.261127166"
     },
     "crai - stub": {
         "content": [
@@ -65,7 +65,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ],
                 "bai": [
                     
@@ -83,15 +83,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:51:45.931558"
+        "timestamp": "2024-09-16T08:21:12.653194876"
     },
     "bai - stub": {
         "content": [
@@ -112,7 +112,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ],
                 "bai": [
                     [
@@ -130,28 +130,28 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:51:34.807525"
+        "timestamp": "2024-09-16T08:21:01.854932651"
     },
     "csi": {
         "content": [
             "test.paired_end.sorted.bam.csi",
             [
-                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:52:55.688799"
+        "timestamp": "2024-09-16T08:20:51.485364222"
     },
     "crai": {
         "content": [
@@ -172,7 +172,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ],
                 "bai": [
                     
@@ -190,15 +190,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:51:17.609533"
+        "timestamp": "2024-09-16T08:20:40.518873972"
     },
     "bai": {
         "content": [
@@ -219,7 +219,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ],
                 "bai": [
                     [
@@ -237,14 +237,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                    "versions.yml:md5,5e09a6fdf76de396728f877193d72315"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T16:51:04.16585"
+        "timestamp": "2024-09-16T08:20:21.184050361"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml
index 0800e05e..62054fc9 100644
--- a/modules/nf-core/samtools/merge/environment.yml
+++ b/modules/nf-core/samtools/merge/environment.yml
@@ -1,10 +1,8 @@
-name: samtools_merge
-
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
-
 dependencies:
-  - bioconda::htslib=1.20
-  - bioconda::samtools=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf
index c60147ed..b08fc5f6 100644
--- a/modules/nf-core/samtools/merge/main.nf
+++ b/modules/nf-core/samtools/merge/main.nf
@@ -4,21 +4,21 @@ process SAMTOOLS_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
-    tuple val(meta), path(input_files, stageAs: "?/*")
+    tuple val(meta), path(input_files)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
-    val(index_type)
-    
+
     output:
-    tuple val(meta), path("${prefix}.bam")  , optional:true, emit: bam
-    tuple val(meta), path("${prefix}.cram") , optional:true, emit: cram
-    tuple val(meta), path("*.${index_type}"), optional:true, emit: index
-    tuple val(meta), path("*.crai")         , optional:true, emit: crai
-    path  "versions.yml"                                   , emit: versions
+    tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
+    tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
+    tuple val(meta), path("*.bai")         , optional:true, emit: bai
+    tuple val(meta), path("*.crai")        , optional:true, emit: crai
+    path  "versions.yml"                                  , emit: versions
+
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +27,7 @@ process SAMTOOLS_MERGE {
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
     def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
+    def input = (input_files.collect().size() > 1) ? input_files.sort { it.name } : input_files
     def reference = fasta ? "--reference ${fasta}" : ""
     """
     samtools \\
@@ -34,8 +35,8 @@ process SAMTOOLS_MERGE {
         --threads ${task.cpus-1} \\
         $args \\
         ${reference} \\
-        ${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_type} \\
-        $input_files
+        ${prefix}.${file_type}##idx##${prefix}.${file_type}.bai \\
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -47,9 +48,10 @@ process SAMTOOLS_MERGE {
     def args = task.ext.args   ?: ''
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
-    def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.${index_type}" : ""
+    def index_type = "bai"
+    def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : ""
     """
-    touch ${prefix}.${file_type}.${index_type}
+    touch ${prefix}.${file_type}
     ${index}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml
index 2e8f3dbb..235aa219 100644
--- a/modules/nf-core/samtools/merge/meta.yml
+++ b/modules/nf-core/samtools/merge/meta.yml
@@ -15,60 +15,81 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_files:
-      type: file
-      description: BAM/CRAM file
-      pattern: "*.{bam,cram,sam}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: Reference file the CRAM was created with (optional)
-      pattern: "*.{fasta,fa}"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fai:
-      type: file
-      description: Index of the reference file the CRAM was created with (optional)
-      pattern: "*.fai"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_files:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram,sam}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference file the CRAM was created with (optional)
+        pattern: "*.{fasta,fa}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: Index of the reference file the CRAM was created with (optional)
+        pattern: "*.fai"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: BAM file
-      pattern: "*.{bam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.bam:
+          type: file
+          description: BAM file
+          pattern: "*.{bam}"
   - cram:
-      type: file
-      description: CRAM file
-      pattern: "*.{cram}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.cram:
+          type: file
+          description: CRAM file
+          pattern: "*.{cram}"
   - csi:
-      type: file
-      description: BAM index file (optional)
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: BAM index file (optional)
+          pattern: "*.csi"
   - crai:
-      type: file
-      description: CRAM index file (optional)
-      pattern: "*.crai"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: CRAM index file (optional)
+          pattern: "*.crai"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@yuukiiwa "
diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff
index d252e1bd..e4e6434d 100644
--- a/modules/nf-core/samtools/merge/samtools-merge.diff
+++ b/modules/nf-core/samtools/merge/samtools-merge.diff
@@ -1,64 +1,57 @@
 Changes in module 'nf-core/samtools/merge'
+'modules/nf-core/samtools/merge/meta.yml' is unchanged
+Changes in 'samtools/merge/main.nf':
 --- modules/nf-core/samtools/merge/main.nf
 +++ modules/nf-core/samtools/merge/main.nf
-@@ -11,14 +11,14 @@
-     tuple val(meta), path(input_files, stageAs: "?/*")
+@@ -8,14 +8,14 @@
+         'biocontainers/samtools:1.21--h50ea8bc_0' }"
+ 
+     input:
+-    tuple val(meta), path(input_files, stageAs: "?/*")
++    tuple val(meta), path(input_files)
      tuple val(meta2), path(fasta)
      tuple val(meta3), path(fai)
--
-+    val(index_type)
-+    
+ 
      output:
--    tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
--    tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
+     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
+     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
 -    tuple val(meta), path("*.csi")         , optional:true, emit: csi
--    tuple val(meta), path("*.crai")        , optional:true, emit: crai
--    path  "versions.yml"                                  , emit: versions
--
-+    tuple val(meta), path("${prefix}.bam")  , optional:true, emit: bam
-+    tuple val(meta), path("${prefix}.cram") , optional:true, emit: cram
-+    tuple val(meta), path("*.${index_type}"), optional:true, emit: index
-+    tuple val(meta), path("*.crai")         , optional:true, emit: crai
-+    path  "versions.yml"                                   , emit: versions
++    tuple val(meta), path("*.bai")         , optional:true, emit: bai
+     tuple val(meta), path("*.crai")        , optional:true, emit: crai
+     path  "versions.yml"                                  , emit: versions
  
-     when:
-     task.ext.when == null || task.ext.when
-@@ -34,7 +34,7 @@
+@@ -27,6 +27,7 @@
+     def args = task.ext.args   ?: ''
+     prefix   = task.ext.prefix ?: "${meta.id}"
+     def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
++    def input = (input_files.collect().size() > 1) ? input_files.sort { it.name } : input_files
+     def reference = fasta ? "--reference ${fasta}" : ""
+     """
+     samtools \\
+@@ -34,8 +35,8 @@
          --threads ${task.cpus-1} \\
          $args \\
          ${reference} \\
 -        ${prefix}.${file_type} \\
-+        ${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_type} \\
-         $input_files
+-        $input_files
++        ${prefix}.${file_type}##idx##${prefix}.${file_type}.bai \\
++        $input
  
      cat <<-END_VERSIONS > versions.yml
-@@ -47,10 +47,9 @@
+     "${task.process}":
+@@ -47,7 +48,7 @@
      def args = task.ext.args   ?: ''
      prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
      def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
 -    def index_type = file_type == "bam" ? "csi" : "crai"
--    def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : ""
-+    def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.${index_type}" : ""
++    def index_type = "bai"
+     def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : ""
      """
--    touch ${prefix}.${file_type}
-+    touch ${prefix}.${file_type}.${index_type}
-     ${index}
- 
-     cat <<-END_VERSIONS > versions.yml
-
---- modules/nf-core/samtools/merge/environment.yml
-+++ modules/nf-core/samtools/merge/environment.yml
-@@ -1,8 +1,10 @@
- name: samtools_merge
-+
- channels:
-   - conda-forge
-   - bioconda
-   - defaults
-+
- dependencies:
-+  - bioconda::htslib=1.20
-   - bioconda::samtools=1.20
--  - bioconda::htslib=1.20
+     touch ${prefix}.${file_type}
 
+'modules/nf-core/samtools/merge/environment.yml' is unchanged
+'modules/nf-core/samtools/merge/tests/tags.yml' is unchanged
+'modules/nf-core/samtools/merge/tests/index.config' is unchanged
+'modules/nf-core/samtools/merge/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/samtools/merge/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
index 17bc846f..0a41e01a 100644
--- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
@@ -80,14 +80,14 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:35.851936597"
+        "timestamp": "2024-09-16T09:16:30.476887194"
     },
     "bams_csi": {
         "content": [
@@ -124,14 +124,14 @@
     "bams_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:41.405707643"
+        "timestamp": "2024-09-16T09:16:52.203823961"
     },
     "bam_cram": {
         "content": [
@@ -158,14 +158,14 @@
     "bams_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:51.695689923"
+        "timestamp": "2024-09-16T08:29:57.524363148"
     },
     "crams_bam": {
         "content": [
@@ -182,14 +182,14 @@
     "crams_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:30.185392319"
+        "timestamp": "2024-09-16T09:16:06.977096207"
     },
     "bam_csi": {
         "content": [
diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml
index 36a12eab..62054fc9 100644
--- a/modules/nf-core/samtools/sort/environment.yml
+++ b/modules/nf-core/samtools/sort/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_sort
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 8e019099..caf3c61a 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -4,19 +4,19 @@ process SAMTOOLS_SORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta) , path(bam)
     tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*.bam"),     emit: bam,  optional: true
-    tuple val(meta), path("*.cram"),    emit: cram, optional: true
-    tuple val(meta), path("*.crai"),    emit: crai, optional: true
-    tuple val(meta), path("*.csi"),     emit: csi,  optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.bam"),  emit: bam,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,  optional: true
+    path  "versions.yml",            emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +32,6 @@ process SAMTOOLS_SORT {
 
     """
     samtools cat \\
-        --threads $task.cpus \\
         ${bam} \\
     | \\
     samtools sort \\
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 341a7d0e..a9dbec5a 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -15,52 +15,73 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 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(s)
-      pattern: "*.{bam,cram,sam}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: Reference genome FASTA file
-      pattern: "*.{fa,fasta,fna}"
-      optional: true
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file(s)
+        pattern: "*.{bam,cram,sam}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference genome FASTA file
+        pattern: "*.{fa,fasta,fna}"
+        optional: true
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: Sorted BAM file
-      pattern: "*.{bam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Sorted BAM file
+          pattern: "*.{bam}"
   - cram:
-      type: file
-      description: Sorted CRAM file
-      pattern: "*.{cram}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.cram":
+          type: file
+          description: Sorted CRAM file
+          pattern: "*.{cram}"
   - crai:
-      type: file
-      description: CRAM index file (optional)
-      pattern: "*.crai"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: CRAM index file (optional)
+          pattern: "*.crai"
   - csi:
-      type: file
-      description: BAM index file (optional)
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: BAM index file (optional)
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/samtools/sort/samtools-sort.diff b/modules/nf-core/samtools/sort/samtools-sort.diff
new file mode 100644
index 00000000..1a6d1649
--- /dev/null
+++ b/modules/nf-core/samtools/sort/samtools-sort.diff
@@ -0,0 +1,22 @@
+Changes in module 'nf-core/samtools/sort'
+'modules/nf-core/samtools/sort/meta.yml' is unchanged
+'modules/nf-core/samtools/sort/main.nf' is unchanged
+Changes in 'samtools/sort/environment.yml':
+--- modules/nf-core/samtools/sort/environment.yml
++++ modules/nf-core/samtools/sort/environment.yml
+@@ -1,6 +1,8 @@
++name: samtools_sort
+ channels:
+   - conda-forge
+   - bioconda
++  - defaults
+ dependencies:
+   - bioconda::samtools=1.20
+   - bioconda::htslib=1.20
+
+'modules/nf-core/samtools/sort/tests/tags.yml' is unchanged
+'modules/nf-core/samtools/sort/tests/nextflow_cram.config' is unchanged
+'modules/nf-core/samtools/sort/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/samtools/sort/tests/nextflow.config' is unchanged
+'modules/nf-core/samtools/sort/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
index c2ea9c72..b05e6691 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -39,6 +39,40 @@ nextflow_process {
         }
     }
 
+    test("multiple bam") {
+
+        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/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                        process.out.versions
+                ).match()}
+            )
+        }
+    }
+
     test("cram") {
 
         config "./nextflow_cram.config"
@@ -98,6 +132,36 @@ nextflow_process {
         }
     }
 
+    test("multiple bam - stub") {
+
+        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/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("cram - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index da38d5d1..469891fe 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -20,14 +20,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T17:19:37.196205"
+        "timestamp": "2024-09-16T08:49:58.207549273"
     },
     "bam - stub": {
         "content": [
@@ -57,7 +57,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ],
                 "bam": [
                     [
@@ -84,15 +84,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T15:54:46.580756"
+        "timestamp": "2024-09-16T08:50:08.630951018"
     },
     "cram - stub": {
         "content": [
@@ -122,7 +122,7 @@
                     
                 ],
                 "4": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ],
                 "bam": [
                     
@@ -149,15 +149,110 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T15:57:30.505698"
+        "timestamp": "2024-09-16T08:50:19.061912443"
+    },
+    "multiple bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:59:55.479443"
+    },
+    "multiple bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:36:13.781404"
     },
     "bam": {
         "content": [
@@ -167,7 +262,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400"
+                    "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc"
                 ]
             ],
             [
@@ -180,13 +275,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-07-22T15:54:25.872954"
+        "timestamp": "2024-10-08T11:59:46.372244"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index 150c3777..62054fc9 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_view
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index dc611448..37e05cec 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:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(index)
diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
index 27be60d0..caa7b015 100644
--- a/modules/nf-core/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -15,77 +15,120 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - index:
-      type: file
-      description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
-      pattern: "*.{.bai,.csi,.crai}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: Reference file the CRAM was created with (optional)
-      pattern: "*.{fasta,fa}"
-  - qname:
-      type: file
-      description: Optional file with read names to output only select alignments
-      pattern: "*.{txt,list}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+    - index:
+        type: file
+        description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
+        pattern: "*.{.bai,.csi,.crai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: Reference file the CRAM was created with (optional)
+        pattern: "*.{fasta,fa}"
+  - - qname:
+        type: file
+        description: Optional file with read names to output only select alignments
+        pattern: "*.{txt,list}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: optional filtered/converted BAM file
-      pattern: "*.{bam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.bam:
+          type: file
+          description: optional filtered/converted BAM file
+          pattern: "*.{bam}"
   - cram:
-      type: file
-      description: optional filtered/converted CRAM file
-      pattern: "*.{cram}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.cram:
+          type: file
+          description: optional filtered/converted CRAM file
+          pattern: "*.{cram}"
   - sam:
-      type: file
-      description: optional filtered/converted SAM file
-      pattern: "*.{sam}"
-  # bai, csi, and crai are created with `--write-index`
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.sam:
+          type: file
+          description: optional filtered/converted SAM file
+          pattern: "*.{sam}"
   - bai:
-      type: file
-      description: optional BAM file index
-      pattern: "*.{bai}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.${file_type}.bai:
+          type: file
+          description: optional BAM file index
+          pattern: "*.{bai}"
   - csi:
-      type: file
-      description: optional tabix BAM file index
-      pattern: "*.{csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.${file_type}.csi:
+          type: file
+          description: optional tabix BAM file index
+          pattern: "*.{csi}"
   - crai:
-      type: file
-      description: optional CRAM file index
-      pattern: "*.{crai}"
-  # unselected and unselected_index are created when passing a qname
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.${file_type}.crai:
+          type: file
+          description: optional CRAM file index
+          pattern: "*.{crai}"
   - unselected:
-      type: file
-      description: optional file with unselected alignments
-      pattern: "*.unselected.{bam,cram,sam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.unselected.${file_type}:
+          type: file
+          description: optional file with unselected alignments
+          pattern: "*.unselected.{bam,cram,sam}"
   - unselected_index:
-      type: file
-      description: index for the "unselected" file
-      pattern: "*.unselected.{bai,csi,crai}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.unselected.${file_type}.{bai,csi,crsi}:
+          type: file
+          description: index for the "unselected" file
+          pattern: "*.unselected.{bai,csi,crai}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@joseespinosa"
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap
index 6bcce9fe..63849b03 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap
@@ -56,14 +56,14 @@
     "bam_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:20.390692583"
+        "timestamp": "2024-09-16T09:26:24.461775464"
     },
     "cram_to_bam_index_cram": {
         "content": [
@@ -169,6 +169,16 @@
         },
         "timestamp": "2024-02-12T19:37:56.490286"
     },
+    "cram_to_bam_index_qname_unselected_csi": {
+        "content": [
+            "test.unselected.bam.csi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T19:38:23.328458"
+    },
     "bam_csi": {
         "content": [
             [
@@ -208,14 +218,14 @@
     "cram_to_bam_index_qname_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:15.007493874"
+        "timestamp": "2024-09-16T09:25:51.953436682"
     },
     "cram_to_bam_bam": {
         "content": [
@@ -240,14 +250,14 @@
     "cram_to_bam_index_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:09.472376824"
+        "timestamp": "2024-09-16T09:25:14.475388399"
     },
     "cram_to_bam_bai": {
         "content": [
@@ -264,14 +274,14 @@
     "cram_to_bam_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:04.080050906"
+        "timestamp": "2024-09-16T09:24:49.673441798"
     },
     "cram_bam": {
         "content": [
@@ -378,14 +388,14 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:52.978954857"
+        "timestamp": "2024-09-16T09:23:27.151650338"
     },
     "cram_to_bam_index_qname_cram": {
         "content": [
@@ -450,14 +460,24 @@
     "cram_versions": {
         "content": [
             [
-                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
+                "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07"
             ]
         ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T09:24:12.95416913"
+    },
+    "cram_to_bam_index_qname_unselected": {
+        "content": [
+            "test.unselected.bam"
+        ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "23.04.3"
         },
-        "timestamp": "2024-05-28T15:42:58.400776109"
+        "timestamp": "2024-02-12T19:38:23.322874"
     },
     "bam_sam": {
         "content": [
diff --git a/modules/nf-core/severus/environment.yml b/modules/nf-core/severus/environment.yml
new file mode 100644
index 00000000..49e4fbc2
--- /dev/null
+++ b/modules/nf-core/severus/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::severus=1.1"
diff --git a/modules/nf-core/severus/main.nf b/modules/nf-core/severus/main.nf
new file mode 100644
index 00000000..e0cc2736
--- /dev/null
+++ b/modules/nf-core/severus/main.nf
@@ -0,0 +1,89 @@
+process SEVERUS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/severus:1.1--pyhdfd78af_0':
+        'biocontainers/severus:1.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(target_input), path(target_index), path(control_input), path(control_index), path(vcf)
+    tuple val(meta2), path(bed)
+
+    output:
+    tuple val(meta), path("${prefix}/severus.log")                              , emit: log
+    tuple val(meta), path("${prefix}/read_qual.txt")                            , emit: read_qual
+    tuple val(meta), path("${prefix}/breakpoints_double.csv")                   , emit: breakpoints_double
+    tuple val(meta), path("${prefix}/read_alignments")                          , emit: read_alignments                  , optional: true
+    tuple val(meta), path("${prefix}/read_ids.csv")                             , emit: read_ids                         , optional: true
+    tuple val(meta), path("${prefix}/severus_collaped_dup.bed")                 , emit: collapsed_dup                    , optional: true
+    tuple val(meta), path("${prefix}/severus_LOH.bed")                          , emit: loh                              , optional: true
+    tuple val(meta), path("${prefix}/all_SVs/severus_all.vcf")                  , emit: all_vcf                          , optional: true
+    tuple val(meta), path("${prefix}/all_SVs/breakpoints_clusters_list.tsv")    , emit: all_breakpoints_clusters_list    , optional: true
+    tuple val(meta), path("${prefix}/all_SVs/breakpoints_clusters.tsv")         , emit: all_breakpoints_clusters         , optional: true
+    tuple val(meta), path("${prefix}/all_SVs/plots/severus_*.html")             , emit: all_plots                        , optional: true
+    tuple val(meta), path("${prefix}/somatic_SVs/severus_all.vcf")              , emit: somatic_vcf                      , optional: true
+    tuple val(meta), path("${prefix}/somatic_SVs/breakpoints_clusters_list.tsv"), emit: somatic_breakpoints_clusters_list, optional: true
+    tuple val(meta), path("${prefix}/somatic_SVs/breakpoints_clusters.tsv")     , emit: somatic_breakpoints_clusters     , optional: true
+    tuple val(meta), path("${prefix}/somatic_SVs/plots/severus_*.html")         , emit: somatic_plots                    , optional: true
+    path "versions.yml"                                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    def control = control_input ? "--control-bam ${control_input}" : ""
+    def vntr_bed = bed ? "--vntr-bed ${bed}" : ""
+    def phasing_vcf = vcf ? "--phasing-vcf ${vcf}" : ""
+    """
+    severus \\
+        $args \\
+        --threads $task.cpus \\
+        --target-bam $target_input \\
+        $vntr_bed \\
+        $control \\
+        $phasing_vcf \\
+        --out-dir ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        severus: \$(severus --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/all_SVs/plots
+    mkdir -p ${prefix}/somatic_SVs/plots
+
+    touch ${prefix}/severus_collaped_dup.bed
+    touch ${prefix}/severus.log
+    touch ${prefix}/severus_LOH.bed
+    touch ${prefix}/read_alignments
+    touch ${prefix}/read_ids.csv
+    touch ${prefix}/read_qual.txt
+    touch ${prefix}/breakpoints_double.csv
+    touch ${prefix}/all_SVs/severus_all.vcf
+    touch ${prefix}/all_SVs/breakpoints_clusters_list.tsv
+    touch ${prefix}/all_SVs/breakpoints_clusters.tsv
+    touch ${prefix}/all_SVs/plots/severus_0.html
+    touch ${prefix}/all_SVs/plots/severus_1.html
+    touch ${prefix}/somatic_SVs/severus_somatic.vcf
+    touch ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv
+    touch ${prefix}/somatic_SVs/breakpoints_clusters.tsv
+    touch ${prefix}/somatic_SVs/plots/severus_0.html
+    touch ${prefix}/somatic_SVs/plots/severus_1.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        severus: \$(severus --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/severus/meta.yml b/modules/nf-core/severus/meta.yml
new file mode 100644
index 00000000..8ada3548
--- /dev/null
+++ b/modules/nf-core/severus/meta.yml
@@ -0,0 +1,217 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "severus"
+description: Severus is a somatic structural variation (SV) caller for long reads
+  (both PacBio and ONT)
+keywords:
+  - structural
+  - variation
+  - somatic
+  - germline
+  - long-read
+tools:
+  - "severus":
+      description: "A tool for somatic structural variant calling using long reads"
+      homepage: "https://github.com/KolmogorovLab/Severus"
+      documentation: "https://github.com/KolmogorovLab/Severus"
+      tool_dev_url: "https://github.com/KolmogorovLab/Severus"
+      doi: "10.1101/2024.03.22.24304756"
+      licence: ["BSD-3-clause"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - target_input:
+        type: file
+        description: path to one or multiple target BAM/CRAM files (e.g. tumor, must
+          be indexed)
+        pattern: "*.{bam,cram}"
+    - target_index:
+        type: file
+        description: path to one or multiple target BAM/CRAM index files
+        pattern: "*.{bai,crai,csi}"
+    - control_input:
+        type: file
+        description: path to the control BAM/CRAM file (e.g. normal, must be indexed)
+        pattern: "*.{bam,cram}"
+    - control_index:
+        type: file
+        description: path to the control BAM/CRAM file index
+        pattern: "*.{bai,crai,csi}"
+    - vcf:
+        type: file
+        description: path to vcf file used for phasing (if using haplotype specific
+          SV calling
+        pattern: "*.{vcf,vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing tandem repeat regions information
+          e.g. `[ id:'hg38']`
+    - bed:
+        type: file
+        description: path to bed file for tandem repeat regions (must be ordered)
+        pattern: "*.bed"
+output:
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/severus.log:
+          type: file
+          description: Severus log file
+          pattern: "${prefix}/severus.log"
+  - read_qual:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/read_qual.txt:
+          type: file
+          description: Severus read_qual file
+          pattern: "${prefix}/read_qual.txt"
+  - breakpoints_double:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/breakpoints_double.csv:
+          type: file
+          description: Severus breakpoints_double file
+          pattern: "${prefix}/breakpoints_double.csv"
+  - read_alignments:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/read_alignments:
+          type: file
+          description: read alignments file
+          pattern: "${prefix}/read_alignments"
+  - read_ids:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/read_ids.csv:
+          type: file
+          description: read IDs for support reads
+          pattern: "${prefix}/read_ids"
+  - collapsed_dup:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/severus_collaped_dup.bed:
+          type: file
+          description: a bed file with identified collapsed duplication regions
+          pattern: "${prefix}/severus_collaped_dup"
+  - loh:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/severus_LOH.bed:
+          type: file
+          description: a bed file with predicted LOH regions
+          pattern: "${prefix}/severus_LOH.bed"
+  - all_vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/all_SVs/severus_all.vcf:
+          type: file
+          description: VCF file with all SVs (somatic + germline)
+          pattern: "${prefix}/all_SVs/severus_all.vcf"
+  - all_breakpoints_clusters_list:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/all_SVs/breakpoints_clusters_list.tsv:
+          type: file
+          description: Severus breakpoints clusters list file
+          pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv"
+  - all_breakpoints_clusters:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/all_SVs/breakpoints_clusters.tsv:
+          type: file
+          description: Severus breakpoints clusters file
+          pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv"
+  - all_plots:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/all_SVs/plots/severus_*.html:
+          type: file
+          description: Severus plots
+          pattern: "${prefix}/all_SVs/plots/*.html"
+  - somatic_vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/somatic_SVs/severus_all.vcf:
+          type: file
+          description: VCF file with somatic SVs
+          pattern: "${prefix}/somatic_SVs/severus_all.vcf"
+  - somatic_breakpoints_clusters_list:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv:
+          type: file
+          description: Severus somatic breakpoints clusters list file
+          pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv"
+  - somatic_breakpoints_clusters:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/somatic_SVs/breakpoints_clusters.tsv:
+          type: file
+          description: Severus somatic breakpoints clusters file
+          pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv"
+  - somatic_plots:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/somatic_SVs/plots/severus_*.html:
+          type: file
+          description: Severus somatic plots
+          pattern: "${prefix}/somatic_SVs/plots/*.html"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"
diff --git a/modules/nf-core/severus/tests/main.nf.test b/modules/nf-core/severus/tests/main.nf.test
new file mode 100644
index 00000000..ab700a4c
--- /dev/null
+++ b/modules/nf-core/severus/tests/main.nf.test
@@ -0,0 +1,208 @@
+nextflow_process {
+
+    name "Test Process SEVERUS"
+    script "../main.nf"
+    process "SEVERUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "severus"
+
+    test("homo_sapiens - [ bam, bai, [], [], [] ], [[],[]]") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam.bai', checkIfExists: true),
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log.get(0).get(1)).readLines().last().contains("Writing VCF"),
+                    process.out.read_qual,
+                    process.out.breakpoints_double,
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[0..2], // Line 3 contains date
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[4..39],
+                    process.out.all_breakpoints_clusters_list,
+                    process.out.all_breakpoints_clusters,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ bam, bai, bam, bai, [] ], [[],[]]") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log.get(0).get(1)).readLines().last().contains("Writing VCF"),
+                    process.out.read_qual,
+                    process.out.breakpoints_double,
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[0..2], // Line 3 contains date
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[4..39],
+                    process.out.all_breakpoints_clusters_list,
+                    process.out.all_breakpoints_clusters,
+                    process.out.somatic_vcf,
+                    process.out.somatic_breakpoints_clusters_list,
+                    process.out.somatic_breakpoints_clusters,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ bam, bai, bam, bai, vcf ], [[],[]]") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log.get(0).get(1)).readLines().last().contains("Writing VCF"),
+                    process.out.read_qual,
+                    process.out.breakpoints_double,
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[0..2], // Line 3 contains date
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[4..39],
+                    process.out.all_breakpoints_clusters_list,
+                    process.out.all_breakpoints_clusters,
+                    process.out.somatic_vcf,
+                    process.out.somatic_breakpoints_clusters_list,
+                    process.out.somatic_breakpoints_clusters,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ bam, bai, bam, bai, vcf ], [ bed ]") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'bed'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log.get(0).get(1)).readLines().last().contains("Writing VCF"),
+                    process.out.read_qual,
+                    process.out.breakpoints_double,
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[0..2], // Line 3 contains date
+                    file(process.out.all_vcf.get(0).get(1)).readLines()[4..39],
+                    process.out.all_breakpoints_clusters_list,
+                    process.out.all_breakpoints_clusters,
+                    process.out.somatic_vcf,
+                    process.out.somatic_breakpoints_clusters_list,
+                    process.out.somatic_breakpoints_clusters,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ bam, bai, [], [], [] ], [[],[]] - stub") {
+
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true),
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/severus/tests/main.nf.test.snap b/modules/nf-core/severus/tests/main.nf.test.snap
new file mode 100644
index 00000000..a5c527eb
--- /dev/null
+++ b/modules/nf-core/severus/tests/main.nf.test.snap
@@ -0,0 +1,600 @@
+{
+    "homo_sapiens - [ bam, bai, [], [], [] ], [[],[]]": {
+        "content": [
+            false,
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "read_qual.txt:md5,3a99166c04453f184c43c348f530301a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "breakpoints_double.csv:md5,68f6ea1191c90253e56f30023a1fbdbf"
+                ]
+            ],
+            [
+                "##fileformat=VCFv4.2",
+                "##source=Severus v1.1",
+                "##CommandLine= --min-sv-size 1 --min-mapq 0 --min-support 1 --TIN-ratio 1 --threads 2 --target-bam test2.sorted.bam --out-dir test"
+            ],
+            [
+                "##contig=<ID=chr22,length=40001>",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FILTER=<ID=FAIL_LOWSUPP,Description=\"Less number of support, but ok in other samples\">",
+                "##FILTER=<ID=FAIL_MAP_CONS,Description=\"Majority of variant reads have unreliable mappability\">",
+                "##FILTER=<ID=FAIL_CONN_CONS,Description=\"Majority of variant reads have unreliable connections\">",
+                "##FILTER=<ID=FAIL_LOWCOV_OTHER,Description=\"Low variant coverage in other samples\">",
+                "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"SV with precise breakpoints coordinates and length\">",
+                "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"SV with imprecise breakpoints coordinates and length\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END coordinate\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the SV\">",
+                "##INFO=<ID=STRANDS,Number=1,Type=String,Description=\"Breakpoint strandedness\">",
+                "##INFO=<ID=DETAILED_TYPE,Number=1,Type=String,Description=\"Detailed type of the SV\">",
+                "##INFO=<ID=INSLEN,Number=1,Type=Integer,Description=\"Length of the unmapped sequence between breakpoint\">",
+                "##INFO=<ID=MAPQ,Number=1,Type=Integer,Description=\"Median mapping quality of supporting reads\">",
+                "##INFO=<ID=PHASESETID,Number=1,Type=String,Description=\"Matching phaseset ID for phased SVs\">",
+                "##INFO=<ID=HP,Number=1,Type=Integer,Description=\"Matching haplotype ID for phased SVs\">",
+                "##INFO=<ID=CLUSTERID,Number=1,Type=String,Description=\"Cluster ID in breakpoint_graph\">",
+                "##INFO=<ID=INSSEQ,Number=1,Type=String,Description=\"Insertion sequence between breakpoints\">",
+                "##INFO=<ID=MATE_ID,Number=1,Type=String,Description=\"MATE ID for breakends\">",
+                "##INFO=<ID=INSIDE_VNTR,Number=1,Type=String,Description=\"True if an indel is inside a VNTR\">",
+                "##INFO=<ID=ALINGED_POS,Number=1,Type=String,Description=\"Position in the reference\">",
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+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotyping quality\">",
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+                "##FORMAT=<ID=hVAF,Number=3,Type=Float,Description=\"Haplotype specific variant Allele frequency (H0,H1,H2)\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest2.sorted\ttest.sorted.phased",
+                "chr22\t16879\tseverus_DEL0\tN\t<DEL>\t60.0\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=13;END=16892;STRANDS=+-;MAPQ=60.0\tGT:GQ:VAF:hVAF:DR:DV\t0/1:232:0.38:0.38,0.00,0.00:28:17\t0/1:93:0.50:0.00,0.60,0.50:13:13"
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+                "##fileformat=VCFv4.2",
+                "##source=Severus v1.1",
+                "##CommandLine= --min-sv-size 1 --min-mapq 0 --min-support 1 --TIN-ratio 1 --threads 2 --target-bam test2.sorted.bam --control-bam test.sorted.phased.bam --out-dir test"
+            ],
+            [
+                "##contig=<ID=chr22,length=40001>",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FILTER=<ID=FAIL_LOWSUPP,Description=\"Less number of support, but ok in other samples\">",
+                "##FILTER=<ID=FAIL_MAP_CONS,Description=\"Majority of variant reads have unreliable mappability\">",
+                "##FILTER=<ID=FAIL_CONN_CONS,Description=\"Majority of variant reads have unreliable connections\">",
+                "##FILTER=<ID=FAIL_LOWCOV_OTHER,Description=\"Low variant coverage in other samples\">",
+                "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"SV with precise breakpoints coordinates and length\">",
+                "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"SV with imprecise breakpoints coordinates and length\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END coordinate\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the SV\">",
+                "##INFO=<ID=STRANDS,Number=1,Type=String,Description=\"Breakpoint strandedness\">",
+                "##INFO=<ID=DETAILED_TYPE,Number=1,Type=String,Description=\"Detailed type of the SV\">",
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+                "##INFO=<ID=HP,Number=1,Type=Integer,Description=\"Matching haplotype ID for phased SVs\">",
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+                "##INFO=<ID=MATE_ID,Number=1,Type=String,Description=\"MATE ID for breakends\">",
+                "##INFO=<ID=INSIDE_VNTR,Number=1,Type=String,Description=\"True if an indel is inside a VNTR\">",
+                "##INFO=<ID=ALINGED_POS,Number=1,Type=String,Description=\"Position in the reference\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotyping quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=VAF,Number=1,Type=Float,Description=\"Variant allele frequency\">",
+                "##FORMAT=<ID=hVAF,Number=3,Type=Float,Description=\"Haplotype specific variant Allele frequency (H0,H1,H2)\">",
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+                "chr22\t16879\tseverus_DEL0\tN\t<DEL>\t60.0\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=13;END=16892;STRANDS=+-;MAPQ=60.0\tGT:GQ:VAF:hVAF:DR:DV\t0/1:232:0.38:0.38,0.00,0.00:28:17\t0/1:93:0.50:0.00,0.60,0.50:13:13"
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+            [
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+            [
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+            ],
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+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
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+                "##FILTER=<ID=FAIL_CONN_CONS,Description=\"Majority of variant reads have unreliable connections\">",
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+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END coordinate\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the SV\">",
+                "##INFO=<ID=STRANDS,Number=1,Type=String,Description=\"Breakpoint strandedness\">",
+                "##INFO=<ID=DETAILED_TYPE,Number=1,Type=String,Description=\"Detailed type of the SV\">",
+                "##INFO=<ID=INSLEN,Number=1,Type=Integer,Description=\"Length of the unmapped sequence between breakpoint\">",
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+                "##INFO=<ID=CLUSTERID,Number=1,Type=String,Description=\"Cluster ID in breakpoint_graph\">",
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+                "##INFO=<ID=ALINGED_POS,Number=1,Type=String,Description=\"Position in the reference\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotyping quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=VAF,Number=1,Type=Float,Description=\"Variant allele frequency\">",
+                "##FORMAT=<ID=hVAF,Number=3,Type=Float,Description=\"Haplotype specific variant Allele frequency (H0,H1,H2)\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest2.sorted\ttest.sorted.phased",
+                "chr22\t16879\tseverus_DEL0\tN\t<DEL>\t60.0\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=13;END=16892;STRANDS=+-;MAPQ=60.0\tGT:GQ:VAF:hVAF:DR:DV\t0/1:232:0.38:0.38,0.00,0.00:28:17\t0/1:93:0.50:0.00,0.60,0.50:13:13"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,99a20821f27fa27a3ed91d9c3d424c84"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T09:47:36.803934533"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/severus/tests/nextflow.config b/modules/nf-core/severus/tests/nextflow.config
new file mode 100644
index 00000000..a1445109
--- /dev/null
+++ b/modules/nf-core/severus/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'SEVERUS' {
+        ext.args = '--min-sv-size 1 --min-mapq 0 --min-support 1 --TIN-ratio 1'
+    }
+}
diff --git a/modules/nf-core/severus/tests/tags.yml b/modules/nf-core/severus/tests/tags.yml
new file mode 100644
index 00000000..d7e36658
--- /dev/null
+++ b/modules/nf-core/severus/tests/tags.yml
@@ -0,0 +1,2 @@
+severus:
+  - "modules/nf-core/severus/**"
diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml
index db8f3f69..b3d97d0e 100644
--- a/modules/nf-core/sniffles/environment.yml
+++ b/modules/nf-core/sniffles/environment.yml
@@ -1,7 +1,5 @@
-name: sniffles
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::sniffles=2.0.7
+  - bioconda::sniffles=2.4
diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf
index 41bc76c1..a85bd216 100644
--- a/modules/nf-core/sniffles/main.nf
+++ b/modules/nf-core/sniffles/main.nf
@@ -50,7 +50,7 @@ process SNIFFLES {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.snf
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml
index c8b2da7d..b52d45a3 100644
--- a/modules/nf-core/sniffles/meta.yml
+++ b/modules/nf-core/sniffles/meta.yml
@@ -11,59 +11,88 @@ tools:
       documentation: https://github.com/fritzsedlazeck/Sniffles#readme
       tool_dev_url: https://github.com/fritzsedlazeck/Sniffles
       licence: ["MIT"]
+      identifier: biotools:sniffles
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - input:
-      type: file
-      description: BAM or SNF file
-      pattern: "*.{bam, snf}"
-  - bai:
-      type: file
-      description: Index of BAM file
-      pattern: "*.bai"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'fasta' ]
-  - fasta:
-      type: file
-      description: |
-        Reference database in FASTA format
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing tandem repeat file information
-        e.g. [ id:'tandem_repeats' ]
-  - tandem_file:
-      type: file
-      description: |
-        Tandem repeats file in BED format
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - input:
+        type: file
+        description: A single .bam/.cram file - OR - one or more .snf files - OR - a
+          single .tsv file containing a list of .snf files and optional sample ids as
+          input
+        pattern: "*.{bam,cram,snf,tsv}"
+    - index:
+        type: file
+        description: Index of BAM/CAM file
+        pattern: "*.{bai,crai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'fasta' ]
+    - fasta:
+        type: file
+        description: |
+          Reference database in FASTA format
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing tandem repeat information
+          e.g. [ id:'hg38' ]
+    - tandem_file:
+        type: file
+        description: Tandem repeat file
+        pattern: "*.bed"
+  - - vcf_output:
+        type: file
+        description: VCF output file
+        pattern: "*.vcf.gz"
+  - - snf_output:
+        type: file
+        description: SNF output file
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
   - vcf:
-      type: file
-      description: Compressed VCF file
-      pattern: "*.vcf.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.vcf.gz":
+          type: file
+          description: Compressed VCF file
+          pattern: "*.vcf.gz"
+  - tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.vcf.gz.tbi":
+          type: file
+          description: Compressed VCF file index
+          pattern: "*.tbi"
   - snf:
-      type: file
-      description: SNF file
-      pattern: "*.snf"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.snf":
+          type: file
+          description: SNF file
+          pattern: "*.snf"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@christopher-hakkaart"
   - "@yuukiiwa"
 maintainers:
   - "@christopher-hakkaart"
   - "@yuukiiwa"
+  - "@fellen31"
diff --git a/modules/nf-core/sniffles/sniffles.diff b/modules/nf-core/sniffles/sniffles.diff
index 9b748dd3..30d9c425 100644
--- a/modules/nf-core/sniffles/sniffles.diff
+++ b/modules/nf-core/sniffles/sniffles.diff
@@ -1,110 +1,67 @@
 Changes in module 'nf-core/sniffles'
---- modules/nf-core/sniffles/meta.yml
-+++ modules/nf-core/sniffles/meta.yml
-@@ -17,10 +17,10 @@
-       description: |
-         Groovy Map containing sample information
-         e.g. [ id:'test' ]
--  - bam:
-+  - input:
-       type: file
--      description: BAM file
--      pattern: "*.bam"
-+      description: BAM or SNF file
-+      pattern: "*.{bam, snf}"
-   - bai:
-       type: file
-       description: Index of BAM file
-@@ -34,6 +34,15 @@
-       type: file
-       description: |
-         Reference database in FASTA format
-+  - meta3:
-+      type: map
-+      description: |
-+        Groovy Map containing tandem repeat file information
-+        e.g. [ id:'tandem_repeats' ]
-+  - tandem_file:
-+      type: file
-+      description: |
-+        Tandem repeats file in BED format
- output:
-   - meta:
-       type: map
-@@ -46,8 +55,8 @@
-       pattern: "*.vcf.gz"
-   - snf:
-       type: file
--      description: Compressed SNF file
--      pattern: "*.snf.gz"
-+      description: SNF file
-+      pattern: "*.snf"
-   - versions:
-       type: file
-       description: File containing software versions
-
+'modules/nf-core/sniffles/meta.yml' is unchanged
+Changes in 'sniffles/main.nf':
 --- modules/nf-core/sniffles/main.nf
 +++ modules/nf-core/sniffles/main.nf
-@@ -8,14 +8,17 @@
-         'biocontainers/sniffles:2.0.7--pyhdfd78af_0' }"
+@@ -4,16 +4,15 @@
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/sniffles:2.4--pyhdfd78af_0' :
+-        'biocontainers/sniffles:2.4--pyhdfd78af_0' }"
++        'https://depot.galaxyproject.org/singularity/sniffles:2.0.7--pyhdfd78af_0' :
++        'biocontainers/sniffles:2.0.7--pyhdfd78af_0' }"
  
      input:
--    tuple val(meta), path(bam), path(bai)
+-    tuple val(meta), path(input), path(index)
 +    tuple val(meta), path(input), path(bai)
      tuple val(meta2), path(fasta)
+     tuple val(meta3), path(tandem_file)
+     val(vcf_output)
+     val(snf_output)
 -
-+    tuple val(meta3), path(tandem_file)
-+    val(vcf_output)
-+    val(snf_output)
  
      output:
--    tuple val(meta), path("*.vcf"), emit: vcf
--    tuple val(meta), path("*.snf"), emit: snf
--    path "versions.yml"                    , emit: versions
-+    tuple val(meta), path("*.vcf.gz")    , emit: vcf, optional: true
-+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true
-+    tuple val(meta), path("*.snf")       , emit: snf, optional: true
-+    path "versions.yml"                  , emit: versions
- 
-     when:
-     task.ext.when == null || task.ext.when
-@@ -23,14 +26,33 @@
-     script:
-     def args = task.ext.args ?: ''
-     def prefix = task.ext.prefix ?: "${meta.id}"
-+    def reference = fasta ? "--reference ${fasta}" : ""
-+    def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : ''
-+    def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": ''
-+    def snf = snf_output ? "--snf ${prefix}.snf": ''
+     tuple val(meta), path("*.vcf.gz")    , emit: vcf, optional: true
+@@ -31,7 +30,7 @@
+     def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : ''
+     def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": ''
+     def snf = snf_output ? "--snf ${prefix}.snf": ''
+-
 +    
      """
      sniffles \\
--        --input $bam \\
--        --vcf ${prefix}.vcf \\
--        --snf ${prefix}.snf \\
--        --reference $fasta \\
-+        --input $input \\
-+        $reference \\
-         -t $task.cpus \\
-+        $tandem_repeats \\
-+        $vcf \\
-+        $snf \\
+         --input $input \\
+@@ -41,21 +40,18 @@
+         $vcf \\
+         $snf \\
          $args
+-
 +    
-+    cat <<-END_VERSIONS > versions.yml
-+    "${task.process}":
-+        sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //')
-+    END_VERSIONS
-+    """
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+         sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //')
+     END_VERSIONS
+     """
+-
 +    
-+    stub:
-+    def prefix = task.ext.prefix ?: "${meta.id}"
-+    """
-+    touch ${prefix}.vcf.gz
+     stub:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+-    def vcf = vcf_output ? "echo \"\" | gzip > ${prefix}.vcf.gz; touch ${prefix}.vcf.gz.tbi": ''
+-    def snf = snf_output ? "touch ${prefix}.snf": ''
+-
+     """
+-    ${vcf}
+-    ${snf}
++    echo "" | gzip > ${prefix}.vcf.gz
 +    touch ${prefix}.snf
-+
+ 
      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
-         sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //')
 
+'modules/nf-core/sniffles/environment.yml' is unchanged
+'modules/nf-core/sniffles/tests/tags.yml' is unchanged
+'modules/nf-core/sniffles/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/sniffles/tests/nextflow.config' is unchanged
+'modules/nf-core/sniffles/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/sniffles/tests/main.nf.test b/modules/nf-core/sniffles/tests/main.nf.test
new file mode 100644
index 00000000..9560b02d
--- /dev/null
+++ b/modules/nf-core/sniffles/tests/main.nf.test
@@ -0,0 +1,286 @@
+nextflow_process {
+
+    name "Test Process SNIFFLES"
+    script "../main.nf"
+    process "SNIFFLES"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sniffles"
+
+    test("homo_sapiens - [bam, bai], fasta, [], true, false") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.tbi.get(0).get(1)).name,
+                    path(process.out.vcf.get(0).get(1)).linesGzip[0..1],
+                    path(process.out.vcf.get(0).get(1)).linesGzip[4..62],
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, [], false, true") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.snf.get(0).get(1)).name,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, [], true, true") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = true
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.snf.get(0).get(1)).name,
+                    file(process.out.tbi.get(0).get(1)).name,
+                    path(process.out.vcf.get(0).get(1)).linesGzip[0..1],
+                    path(process.out.vcf.get(0).get(1)).linesGzip[4..62],
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, bed, true, true") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ]
+                input[3] = true
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.snf.get(0).get(1)).name,
+                    file(process.out.tbi.get(0).get(1)).name,
+                    path(process.out.vcf.get(0).get(1)).linesGzip[0..1],
+                    path(process.out.vcf.get(0).get(1)).linesGzip[4..62],
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, [], true, false -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, [], false, true -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = false
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, [], true, true -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [[],[]]
+                input[3] = true
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai], fasta, bed, true, true -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ]
+                input[3] = true
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/sniffles/tests/main.nf.test.snap b/modules/nf-core/sniffles/tests/main.nf.test.snap
new file mode 100644
index 00000000..cb690bac
--- /dev/null
+++ b/modules/nf-core/sniffles/tests/main.nf.test.snap
@@ -0,0 +1,481 @@
+{
+    "homo_sapiens - [bam, bai], fasta, bed, true, true -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ],
+                "snf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T12:18:52.803761263"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], true, false": {
+        "content": [
+            [
+                "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+            ],
+            "test.vcf.gz.tbi",
+            [
+                "##fileformat=VCFv4.2",
+                "##source=Sniffles2_2.4"
+            ],
+            [
+                "##contig=<ID=chr22,length=40001>",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend; Translocation\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase-block, zero if none or not phased\">",
+                "##FORMAT=<ID=ID,Number=1,Type=String,Description=\"Individual sample SV ID for multi-sample output\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FILTER=<ID=GT,Description=\"Genotype filter\">",
+                "##FILTER=<ID=SUPPORT_MIN,Description=\"Minimum read support filter\">",
+                "##FILTER=<ID=STDEV_POS,Description=\"SV Breakpoint standard deviation filter\">",
+                "##FILTER=<ID=STDEV_LEN,Description=\"SV length standard deviation filter\">",
+                "##FILTER=<ID=COV_MIN,Description=\"Minimum coverage filter\">",
+                "##FILTER=<ID=COV_MIN_GT,Description=\"Minimum coverage filter (missing genotype)\">",
+                "##FILTER=<ID=COV_CHANGE,Description=\"Coverage change filter\">",
+                "##FILTER=<ID=COV_CHANGE_INS,Description=\"Coverage change filter for INS\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_US,Description=\"Coverage fractional change filter: upstream-start\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_SC,Description=\"Coverage fractional change filter: start-center\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_CE,Description=\"Coverage fractional change filter: center-end\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_ED,Description=\"Coverage fractional change filter: end-downstream\">",
+                "##FILTER=<ID=MOSAIC_AF,Description=\"Mosaic variant allele frequency filter\">",
+                "##FILTER=<ID=NOT_MOSAIC_AF,Description=\"Variant allele frequency filter for non-mosaic\">",
+                "##FILTER=<ID=ALN_NM,Description=\"Length adjusted mismatch filter\">",
+                "##FILTER=<ID=STRAND_BND,Description=\"Strand support filter for BNDs\">",
+                "##FILTER=<ID=STRAND,Description=\"Strand support filter for germline SVs\">",
+                "##FILTER=<ID=STRAND_MOSAIC,Description=\"Strand support filter for mosaic SVs\">",
+                "##FILTER=<ID=SVLEN_MIN,Description=\"SV length filter\">",
+                "##FILTER=<ID=SVLEN_MIN_MOSAIC,Description=\"SV length filter for mosaic SVs\">",
+                "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"Structural variation with precise breakpoints\">",
+                "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"Structural variation with imprecise breakpoints\">",
+                "##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description=\"Structural variation classified as putative mosaic\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of structural variation\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variation\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Mate chromsome for BND SVs\">",
+                "##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description=\"Number of reads supporting the structural variation\">",
+                "##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description=\"Number of reads supporting an INS/DEL SV (non-split events only)\">",
+                "##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description=\"Number of soft-clipped reads putatively supporting the long insertion SV\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of structural variation\">",
+                "##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description=\"Standard deviation of structural variation start position\">",
+                "##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description=\"Standard deviation of structural variation length\">",
+                "##INFO=<ID=COVERAGE,Number=.,Type=Float,Description=\"Coverages near upstream, start, center, end, downstream of structural variation\">",
+                "##INFO=<ID=STRAND,Number=1,Type=String,Description=\"Strands of supporting reads for structural variant\">",
+                "##INFO=<ID=AC,Number=.,Type=Integer,Description=\"Allele count, summed up over all samples\">",
+                "##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description=\"List of read support for all samples\">",
+                "##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description=\"Number of reads that support the generated insertion (INS) consensus sequence\">",
+                "##INFO=<ID=RNAMES,Number=.,Type=String,Description=\"Names of supporting reads (if enabled with --output-rnames)\">",
+                "##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">",
+                "##INFO=<ID=NM,Number=.,Type=Float,Description=\"Mean number of query alignment length adjusted mismatches of supporting reads\">",
+                "##INFO=<ID=PHASE,Number=.,Type=String,Description=\"Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE",
+                "chr22\t1\tSniffles2.INS.0S0\tA\tATTAGGCAAAGAGAATATACTCGACTCATTTTGCTATACAGGAAAAAAGTGCTTCCTTAGCTCATTTGGAAAGAGATTGAGATTAGAAAAGATGGTTAATTTGTATGTATTTATAGAAATAAATAGAATACAAAATGAGGCTTTTAAATTTTTTCCCACATGAAAATATGATTACTTTAATCATTACGTTTTACATTGTTAGTTTGCAGACAGGCATAATTAGGTCCTCAGTTGCAGAAATCACAGACATCTGAAGGCCAGCCCTTTAATTTGGCCACCCCTAGATTTCTCTGCTCCTTCCTTTGCTCCTCCTACTGCACAGTTTGAACTGATGCTGTTCTATATAAGGTACTTTTCCACCTACCTCATCTCTGACTACAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACCATGCCAACAATCAGGGCACCACCTAGCAGAGTCAGTGAAGGCCAAAATAAACAGTGGAAGATAGCCATTTGGTCATACTTTTTTATAAGAATGACATCTTCAGATTGGCTGGCTGGACTGTAGAAGCATGAAAAGGGGGTTCCATTTTTGTGATCGAAGAATTCTTTTATGTCCAGAGCACTGTTGAGCAAATCATTTCTATCTTGGTGGCACTTAGGTGTGTAAAAGCACTAGGAATATGGAAGAGGGAAAAAGATAAAGGCACTGTCACCAATACCAAATACTTAACAGTTTCTAATTATGAAATAGCTTCAGGCTGAAGTTATTAGTGGGCAGTTTCAATCTTAGAAGGTGGTAAAATATTACATAGCTCATGGGAAAGGGTTGATTGGAGGGCCACAGTGAAATGGCCATTTCCAGTCATTAAGCAAGGATGTGGAAGAGAATTCTTAGTTTATATGACATTGCAGGAGAGTCAGTGACCAATTTCATAAGGAATATGACTCCTCCCTACATGCAGGTTCTTGGACTCTTGGACAGTATGAATCCGTTTGTCCATTGAACAAAAATGTATTGAGCCTTACTATGAGCTTTCAACACCTAGTAGTGCCTCTGTGGTCTCTGTCTTGATCTCCTGTAGCAAAATATTACCCTGAAGAAAAGCACGTTGAGGCTTTTGCTCTAGACTCACAGACAGGGAGCCCCACCTGGACTTTGGTTCCTGGGAGACAGAACCAGTGGAGAAGGGAGCTCTGTCAGCTGGTGACTTTTTTAAAAAAGCTTGAGGTTTATTACCATATCCATTAGGTACTTGAGGTACTGTGCTAAAGGCCTACAAACTGTTTGAAATCTTAAAAATCATTGCATCCAAAATAGAAAACAAAAGTCATCAGATTGAAATTGTAGGACTAAAGACAATAAAGTGTAACATGTCAACTAATCTTAACACAACTCAACTTTTATAGTTAGGTATAAATATAAATTTTAAATGATATGAAAGACTATACTTTCAGGGATCATTTCTATAATTCGTTAAATTATATGAACCCATTGTGTAACTTATTAAAATAAAAATAATCTTTACATTTATTTGATAAGAAAAAATTACTCGCTTGATTCAAGGGAGACTGTGGTACACTGTGTAGCATATGTTATATGGCGCGGAGTGGAATCTCCAAAAGAAAGACTCCCCACAAATGACTACTCATTGGCTCAGCCTATAAATTCCAGACACCAAGTTGTGAAATTGGAATAATTTCTCTCCTTTCTATATACCCCATTTCTCCACCAAGAAGAAAGCTTCATTTATCCTGATTTGATCACTATAAAAATGTTCACTCCAAAAAAATAGATTTATCCCTAAAGACAGCCCTGGGTTATTTATGTACCCTGCTAGGGACAGTCTGGCAGGGAAGGGTTGCTGTCATAAGAACTCTTTAAACTTTACAATACCTTGGGATTTATCTGGACAGCCTCTTCATTATAATGTAGGAGAGCTTTCTGAGCTGAATGGGTGAGGTTCACAAACACCCGAAGACACGAGTACTTCCCGTGACCACGGCAGTGCACACCACAGGTGAAGGCACAGTCCAGCCAGTCGTCCATGATATCTGTGTGGATGGCAGTGCAGGTTGATTCTTCTCTCCGAATGCTTCAATTTGAAAAAAAAAAAAATGTTCTTCACTTACTAGAAAATTTCGTTCTACATTTTGGTGCGGTTATGAGCTTATGTACACAATTAGCTGGGATTACAGGCGCTCAGCTGCCATGTCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTGTTGGCCAGGCTCGTCTCCAACTCCTGACCTCAAGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCTGGCCCAAATACTATGTTTTATCAATTCTAAAGTGCACTTTAGTATTTACATTTTAATATAACTAAAATCAATATGTATTTTGCAATCAATGGCATCTTGCTATTATTTGAAAACATTTCTTTAATAGTCTGTAAAATAATGGAACATGCCCAGATGCAGTGGCTTGTGCCTGTAATCCCAGCACTTTGAAGGGTCAAGATAGGAGGATCGCTTGAGCCCAGGAGCTGGAGACCAGCCTGGCCAATATAGTGACAGAATAAATAAATAAGTAAATAAAATAATGGAAAATCTCACAAATGGTGATGTTTTAGGTTCGACAAAATACATTAACTAGCCCATTTAGTTTTCTGAAATTATTTTGATGTTATTGCTTACAATATTTGTTCTGTGGTACACAACCATAGGATTAATAATATTGATGAAAATAATAAAAGAATAATAAGCATGTATTGAGCTCTTCCTGTGTGAAGTTCTGGACAAATCCTCATAAAGCCTTAAAAGGCAGATACTAGGCTGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACGAGGTCAGGAGATTGAGACCATCCTGGCTAACATGATGAAACACGGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCTGAGGTTGCAGTGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGCGACAGAGCAAGACTCTGTCTTAAAAAAAAAAAAAAAAAAGAAAGAAACAGGCAGATACTAGCCCAGGCACGGTGGCTCATGCCTGTAATCCCACACCTTCGAAGGCCCAGGCGGGTGGATTATCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATTGTGAAACCCTGTCTCTACTAAAAATACAAAAATATTAGCCAGGTGTGGTGACAGGTGCCTGTAATTCCAGCTACTCAGGAGGCTAAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATTGTGCCACTTTACTCCAGCCTAGGTGACAGAGGAAGACTCTGTCTCAAAAAAAACAAACAAACAACAACAACAACATCAAAAAGAAACCTATAGTAATAAAATTGAAACAGAAGGAGGTTTGCAATCAAAATGACTGACTAGGAATGAAATAGGAAAACATAATAATTTGCATCTGCATAGGGAAGTCTGAGATTGGCTGATCTTGTTCTCTTCGAGGGGGAATACTAGTCCAGAACTTGGGGTGCCTGCCAAGAGGGGAGCAGCCACAGTAGGAAAGGGGGACTCTGGAATGCTAGGGTTCTGGGGTCTGTGGACACAGGAGGCAGAGGACATGTGTTAAGATGTTTTAAGAAATGAATGTTGAACTGGATATGAAAATATTTTTCAGCCGGGCGCAGTGGCTCACGTCTGTAATCCCAGTACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCCGTCTCTACTGAAAATACAAAAAGTTAGCCAGGCGTGGTGGCGGAGGCCTGTAATCCCAGTTACTCTGGCGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGACGGAGCTTGCAGTGAGCCGAGATTGCGCCTCTGCACTCTAGCCTGGGCGACAGAGGGAGACTCCATCTAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAATATTTTTCACTATAGAGAGGCATATGTCCCCTGAACTTGCCGGGATCCACCTTTCCTGCTGGTGCATTCTGTGAGTTAGAAGAAAACTTCCAAAGAGCCATTTTTTCCACCCTGTCTACTGTATAAAATTGCTTCTCAAACATGTGCTGCATTGCAGAGGATTACCATTGTTTTGCTAACCAGCGTCTGGTCTTTCTTATGTGGCGCTGCAATTACTAGTGTCAAACCCTGTTGGTAATACCCAGAGGATGGTGTCTGAAGTCTTTACTCAATATTCACATTGGCTGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTCGGAAGCAGAGGCAGGCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAAATTAGCCGGGTATGGTGGCGGGTGCCTGTAATCTCAGCTACTAGGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGATTGTGCCACTGTACTCCAGCCTGGGGGAAAATTCACATTTGTAGAGAGTTTAAATTCTTTTTTGATACGGAGTCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCAGGGTCTTGACTCACTACAACCTCTGCCTCCCAGGCTCAAGGGATTCTCCTGCTTTAGCCTCCTGAGTAGTTGGGATTACAGGCACCCACCAAAACACCTGGGCAATTTTTGTATTTTTATTAGAGACAGGGTTTCACCATGTTGTCCAGGCTGATCTGAAACTCCTGACCTCAGGTGATCTGCCTGCCCTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCCGGCCGAGAGTTTAAATTCTTAAATCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCGTCTCAGTATTTCTATTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCAATTCCAGGTAAACTTTGGCCTTTTATGAATTCTCCTGATCAGGCCAAACCTCAACCAAGTCCCTTCTTGATCTTCTCCTTCACCTCCTTCCCTCATTCACCCAACAATTAGCCTCCAGTCCACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAAGCCTCAGCTAAAGTTTACAATCCTACCTTTTCTACTGCCTTGAAATGCCCTAAGGTTCAGGGGCTTCATGGTTGCTGCTTCATGGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCCGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTCTACAGCTCTGCTGTCCCATTAACAGCACCTTTGGGGCCCCAGGGTTCCAGATTGGAAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCTTTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTCTACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAGAGGATCTTTAGCCTGCGGCGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAAGGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGATCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAATAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGAGGAAAGGATGGAAACTACTACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCTTCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGTTTTTGTAGATTGAAGTCTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCCAGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGAAATCCTTCCACCTCAGCCCCCCAAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGTTAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAAGTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGTATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGGCCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCAAATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCATCTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGCTATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGAAGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGGCCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCCCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGAAAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACAGCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAATATCTGAGACCTAGCATGCTAGGAGACCTTTATCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAAATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGATGTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCA\t44\tCOV_CHANGE_INS\tPRECISE;SVTYPE=INS;SVLEN=7407;END=0;SUPPORT=3;COVERAGE=0,0,0,0,8;STRAND=+-;STDEV_LEN=16.000;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t./.:0:0:0",
+                "chr22\t10115\tSniffles2.INS.2S0\tA\tAATGTGAAATTGCAAATAATTCACCTGAGAAATGAAAATTAATCTTCTTTGCTAAATGCCATAGAGATATTTTAAGTTGCTAATGTTACTTAGATGTTCATTAACTTAGTGAGTTACATTAAGTAGAGAAGATGCCTTTTTTTTTTTCTGTACGAAGTCTTGCTCTGTAGCCCAGTGTAGTGGTATGATCTCGGCTCACCACAACCTCCGCCTCCTGTATTCAAGCGACTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGATTACAGGTGTGCACCATCGCACCTAGCTAATTTTTTGTATTTTTAGCAGAGACAGCATTTCACCATGTTGGCCAGGCTGTTCTTGAACCCCCGACCTCAGGTAATCCACCCTCCTTAGCCTCCCAAAGTGCCAGGATTACAGGCGTGAGCCACTGCACCCTGCTGAGAAGATGCCTTTTGACAATGAAGTGGATTTGTATATTTATCTTTGGCTTAAAAAAACATGCACCACCAATTACACTTTCCTCAAGTTTAAATTTTTAATAATTAGGAAAATAAAGCATTTTCTTGTCTTATAGTGTTAGCTAGATTGTTTTTGTGTATTTTGTCATGAATAAAAAGCATAGCTATATAGTTACTGCTTTTACATTAACTATAAATATCTTAAAATTTTACTACCTAAAATCAGGAAACTTGAACTGAAGCTACTAATCTTAGAGTTGGAAAAGTAAATACATAGAGGTTTCCTGTTGTACAAATGTCAAGTGGCACAGTGAAATTTACATTCATTTGAAAGTTTTCCTAACTGTAAAAAGTATCAAATTACTTGATACTTTGGAGTAGTTCATCATCTTTATCAGAGGCACAGGTCTTAACCATTGGCAAGCCTCTGTCAGAATATGCACATATTAAAGATCTGATTATTTTTGTGTTAATGTTAAAAAATTTTTCTGAAGCTTTTATCTTATTTTTTCCATCCTTACACCGTAAATTCACATTACCAAGTTGGGAAGCCAAAGAAACATTCTACTCTACTCATGTTTTTTCACCAGTTCATGAAAGTTGATGTTAGAAATGGGTGTGGGTGTGGGGGATGGGGGTGGTTGTACAGAAGCAGCAGGTGGTAGGGATAGGATTTCTGAAGCACTATCCTTGGCCTTTTTTGAGTAAACTCTTTATACCCTGAGCCACTTTCTTTTCAGAGGGCAATTGCTATTATTAGAGAGCCACCTTAAGCATTATTGTTGTAGAAAAATTAGGCACAACCAGTGATTGTCATTACAAGGACCAGCAAAAATGGCTAGGTTGCTACTCTGTATTTGTAACGCCCTTCCCCCAACAAAATTTCTCCTTTTCATATCTGTGAATTAGAAATAAGTGATAGAAAACTGTACTGCATTACAATATATACCATTTAATAAAACAAGTTTATAGTTGAGAGCACTATTCATGCTTTTTGAAAGAATGCAAATTTGTAATTTTTATGATAGCAATTCTTAATAATTTATTGTCCAAGAGATTTGATAAAATTTTTGATAGTTATTGGTCTCTGGGACTCAATAGGCACTGGAATGTTTTAATTCAGTTGAAAAGTTGGTTCAGGATTGCTACCCTCTCTTACCTGTTAGGAGGTTGTTGTTTAACCTGACCTGAAATTCCCATGAATAAGAACCTGTTTTTTTTTTTTTTTTTCTTTGACAGAGTCTTGCTCTGTCGCCCAGGCTGCAGTGCAGTGGTGCGATCTTGGCTCGCTGCAAGTTCCGCCTCCCAGGTTCAAGCGATTCTCCTGTCTCAGCCTCCCAAGTAGCTGGAGTAGCTGGGACTGCAGGCACGTACCACCATGCCTGACTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCGCAATCTCTTGACCTCATGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCACCTGGCCCAGGGAATTTCTAATATTTGAGAAGATGTTATTTTTAGTCTATTATACAAATTTATATATTGTTTACTAATATATAAATTTACATATTGGTTACTAATATGTAAACACCAATTTACATATTGGTTACTAATATGTAAACTTGATAAACATGGATTTCCATGGAAATTTAAAAGTATCACAACAATTTGTTTTCCCATTCTGAAACTTGTGATTTATTACATTTTCCTACTATTTCAGTTAATTCCATAATGCCAGATTTGTTGTAAATTTGCCGAGTGACAAGCCACACTGCTTCCTCTCATTCCTCTATTCCACAAAACTGCAAAGTTTCCCAGACCACAGTCAGGTTTCTCTGGGTTGTCCACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTAAGTCACTTTAAGTTTATGACGGAGGGGCTTCGTGAAACTTCATTGACCTTCCAAGGTGAAAATTGGTCAGTTTTCAGTTATAAAGGACATTAAGGATGGGTGTGGTGGCTGATACATGTAATCCCAGCACTTTCGGGAGACTCAGTCAGGAGGATCACTTAATCCTCATTTAAAAGGAGTTTGAGACCAGCCTGGGCAACAAAGTGAGGCCTTGTCTCTACAAAAAAATTAGCTGGGTGTGGTGGTAGGCACTTGTAGTCCCAACTACTCTGGAGACTGAGCTGAGAGAAGATTGTGTGAGGCTTGGAGGTTGAGGCTGCAGTGAACGGACATCACACCACTACACTCTAGTCAGGTGACAGAGCAAGACTCTAAATAAATAGGAACATTAGATGGTCTCTCTGCACTCTTGCCTGGTGGGGACGTGTTAGATACCCTCGTTAGGTTGTGATTTAGTTTTTAATCTGTGAGATGTTTGGGTCAAACAATTTTTAGCTGCCATGGAATAAACTTTCCAGTCAACGTGTGAGTTTGTGTTTGCCTTTACTTTTTTTTTTTTCTATATTGTTTTGGTCTATTTTTATCTTTTAATTTCAGAAAGCTGATTAATCTCTTCCTTTTCTCTTTAAAAATTTTCTTTATCATGTTTGTGCTACAGTGGTTATTTTGAGAACTTGTTGGCAGGATAAGTTGCAAAAGTTATGAAGTAGAATAGGGATGATTTCTGTTTTTGTTTTTTTTTTTTTCAGACAGAGTCTCACTCTCTTGCCTAGGCTGGAGTGCAGTGGCGTGATCCTGGCTCACTGCAGCCGCCGCCCTCCGGATTCAAGTGATTTGCCTGGCTCAGCCTCCCAAAAAGCTGGGATTACAGGTGCATGCCACCACACCCAGCTAATTTTTGTGTTTTTAGTAGAGATGGGTGTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCCGCACTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCATGCCTGGCTGAGATTATTTCTTTTTTTATTATAGCCATTGCTTGTAGATATATGCTGGTGGTTATCTGTAAAAATGTAATAGAAAGGCCGGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACAAGGTCAGGAGTGGGAGACCAGCCTGGCCAATATGGTAAAACCCCGTCTCTACCAAAAATACAAAAATTAGCTGGGCATAGTGGCGGGCACCTATAGTCCCAGTGACTCGGGAAGCTGAGGCAGGACAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGATCGTGCTATTATTGCACACCAGCCTGGGCGACAGAGTGAGACTCCGTCTCAAAAAAGAAAAAAGTAATAGACCAATCTTGAATTTATAATTGGAAGTGTTATTTCTTTATTTGCAGAATTTATTTATTTGTGACGCAGCTGTTGCTACCTCGCCTTTTCTTTTGTTGAGCTTAATCTCATGTCAAGTCATTCAACCAACTCAAAAGCGATGAAGACATTATTGAATCAACCTGAACTAAATCAGACCTAGGCTTCTTAAAATATACAGCTTAATGCTTCCAAATGATTTAGAAAACTAAAAAACCTAGCTACGCTGTAGGACACACAGTGGCCAATAAAAACAGGACCCCCAAACTGGCCAGTGGACCACTGCAACCACTATTTACTTCCTCCGTGTTTAGGAATGTTCAACGCTCCAAGCCCCATAGGCTGATTCAAGAAGATAAAGTGAGACTCAAGGAATTTCGAAGTGGAACAATACACCAAAGCCTTAAACCTGAAATGACTCTCCTTTTCTGGGGGTGAGGGAAGAAAAAGAAAAAGTTTCTAGGGCTCTCGGGGTGGCCTGGATGCCAGGGTCCCAGAAGTGGCCTTTTCTAGCTCCTGTAACTAAACCTGGCGGAAAACTCCCCGCCTGCTCACTCCACCCCCACCCGCCCAAGAATGCGTCTTCCCGTCTTCGGTGGCCCTACCCAGAATCCCAAAATGTGGGTTCCAACCCGGGCCCTGAATGTCTTCTCAAATCCCCGGGACCCAGGTTCCGGTGCGTGCCTTGCGTGCCGGGTCTTGCCCCTCGGGCGGTACCACCCAGGCAGCCCTAAATCCAGCCTCCCGGGCCCCCAGCAGCGCCCTCCGCCCCTCCACTATCCGGTCCGGCTCGAAGTCGGGGCCAAATCCAGAGACAAGAGGGCTGTGCCTGAAACTGAGCAGTTTCACCACTCGGCACTCCTGGCGGAAACTTCCCTTTAAAAAAAAAAAAAAAGAAAAGAAAGAAAAGCAACAGCACTTTTGGGCTAGCATTTCAATCCTTCCTGCCCTTTAGAGTTCCCAGTTCTGCTTCCAGCTGGCTTTGGGTGTTCCACTAGAATTGAGTTGTAAAGATATTCTTTAAGTGTTTATAGAACATTAAGACTTAAAAAAAATCTTTAAAATTAGAGGAGGGAAGCCACTGATCGCACACATCCAGGAAATGCAGCCCCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGACTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCGGTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGATCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAACTTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCCGCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTTCGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGATTCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGAGCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGGAAGCGCAGGAGCCGGCTGGGGGAGGGGGCGCCCTAGAGAAGCGGCTAGAAAGCTGAGACGGGGAACTGAGGTCATCCTGGGGGGGACAAGACAATGAGAGCCGGGCGCCTTGGGGGCGGCGCGGGAGCCTCCGCAGGACCAGGCGGGCGCCCCCTTTACCTGCGGCTCCGGCGCCTCGGCCGTTTCCTCGCGCGGCGGCGGCCGGGACTGAGCTGACACCACTCAGCCGGCGGGGTTTGAATGAGGAGGAGCGGGCGCGGAGGGGAGGGGGCGGGGAGGGAGGGAGGGAGGCGTCGCGGAGTTTCTCTCGGCCTTTTGTGCCATCCGCCGAGGCGCCTTGAGTATAAATCCAGATAGTGCAGTTTTTGTTGTGCTTGTGCTGATCAACTTTATGGTGTGATTAAATACGATTTTTTTTATTACGCTCTTGAAATTGTACTCTTGAGGTTGCAGAATGGCAATTAGATGGCAGTCGCTGATAGCCATGTAGAAGTTTTGATGAACATGCAAGTTAATTTTAATTTCTGATCAGTTACGGTTAGTGACTGTGGCCAAACATGTGCGTACTGATTCTACATGTGCTAATTCCGTGACGTTTATTCACCAGCTATGTGTCCCGTGCCTAATCCTGTGTCAGGCACCTTGTTCCAGGCATTGGGGGCAGCAGTGGACAAGGCAACAGAGTCTCCATCCTGAGGTGTTACTTTTAGAAAAAGATAGTTACAAGCAAATAAACAGGATGGTTTTAGATCTGGACAGAGGTTTTCAGAGGAAGTCATCCTTGAGCTGTCACAATGCTTTGGGGAGGGGTGTGCTGGGTAATCAGGGATGGCACATTTGGGGTGCCTAAGGATTGCTGTGGCCCTGGGAGCCTAGGACAGTTGGTCACAATTGACTTATTAGAGTCAGTCTCAGAAGCTTTCCTGGAAGTAGAATTGCTGCTGTTTTGCCAGGAGGGTTTCCTTCCCCATCTGACCACACAAGAAGACCCCTGCCCACAAATGCCTACCACTCCCAGGTCTCCCAGGCTGTTCACCCTCCCAGGCAAAGTGGAAGCTTCCTCTGTCCTAAGATCGTTTCCCACTGAACCTCCTTCATTTTCCTTCACTGCAGAGAAATAATCCTACAAGGTCTTGTGTGGAGAGTGATGGTACCTTCTTTAACCCAGATAATTGAGAATTGGAACCAAAACATCTGTGTATTAATAAATATTTTCAGTAACTAGGTTATGCTATTTCCCTGAGTGGGAAATAACACTCCATCATGTTTCTTTTTTTGGGGGGCAAGGGGGAGTCAAAGTTGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCGTGACTTGCACATATACATCCAGATGGCCTGAAGTAATTGAAGATCCACAGAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAATCTCCCCCACCCTTAAGAAGGTTCTTTGGAGTCTCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGACTGTAATTTTCCATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTCCCTTCACTTGACTCTCTTTTCAGACTCAGCCCACCTGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACGAAGCCTGTTTGGTGGTCTCTTCACACGGATGCGCATGAAATTTGGTGCCGTGACTTGGATCGGGGGACCTCCCTTAGGAGATCAATCCCCTGTCCTCCTGCTCTTTGCTCCGTGAGAAAGATCCACCTACGACCTCAGGTCCTCAGACCGACCAGCCCAAGAAACATCTCACCAATTTCAAATCTGGTAAGCGGCCTCTTTTTACTCTCTTCTCCATTCCTCCTCCTTCTCCCTTAGCTTCTCCAACCTCCCTCACTATCCCTCAACCTCTTTCTCCTTTCAATCTTGGCGCCACACTTCA\t7\tPASS\tPRECISE;SVTYPE=INS;SVLEN=7453;END=10115;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.300;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/1:10:7:3",
+                "chr22\t10126\tSniffles2.INS.1S0\tA\tACCGCTTTTCTGGGGCAGGGGCAAGTACCCCTCAACCCCTTCCCCTTCACACTTAGTGGCAAGTCCCGCTTTCCTGGGCAGGGGCAAGTACCCCTCAACGCCTTCTCCTTCACCCTTAGTGGCAAGTCCCGCTTTTCTAGGGGGGCAAGAACCCCCAAACCCCTTCCATCTGTGTCTCTACGCTCTCTTCTGTGGGTTTGCTTCCTTCACTATGGAACCTTCCACCCTCCATTCCTCCTTCTTCTCCCTTAGCCTGTGTGCTCAAAAAGTTAAAACCTCTTCAACTCACACCTGACCTAAAACCTAAATGCCTTATTTTCTTCTGCAACACCGCATATCTTGCTTGGCCCCAATACAAACTTGACAATGTCTCTAAATGGCCGGAAAATGGCACTTTGATTTCCCCACTGACAAACACCTAAATAATTTTTGTCGAAAAATGGGCAAATGGTCTGAGGTGCCTTACGTCCAGGCATTTTTCACACTTCGTTCCCTCCCTAGTCTCTGTTCCCAATGCGATTCCTCCCAGATCCTCCTCCTTTCCTCTCCTGTCCCCTCGGTCCCAACCCCAAGCGTCGCTGAGTCTTCCCAGTCTTCCTTTTCTACAGACCCATCTGACCTTTCCCCTCCTCCCCAAGCTGCTTGTCGCCAGACCGAGCTAAGTCCCAAGTACCTCCCTCAACTCTCCACTCCTCCACCCTATAATCCTTCTATCACCTCCCCTCCTCACACCTGGTCCGGCTTACAGTTTAGTTCCGCGACTAGCGCTTCCCCACCTGCCCAACAATTTCCTCTTAGAGAAAGTGGCTGGAGCTGAAGGCATAGTCAAGGGACATGTACTTTTTTCTCTATCAGACCTCTCTCAGATCAGTCAATGTTTAGGCTCTTTCTCATCAGACCCCACTAAATATATACAGGAATTCCAATATCTAACTCTGTCCTACAACTTAACCTGGAGTGACTTAAATGTCATCCTGACTTCTACTCTCTCCCCAATATGAACGGGAAAGTTTTTTCTCTAGCCCAATCTCGTGCTGATAACCGCCGGCTTCATGAGCCAGACCTCCAGGAAGGCATTAGAGCAGTTCCCCGAGAGGATCCCCAATGGAACTATCAGGCAGATTCCCCAGGTACAGCTAGGCGAGATTACATGGTTTCCTGCCTAGTTGAAGGGCTTAAAAAAGCAGCTTACAAAGCTGTTAATTATGACAAGCTTAAAGAAACTACCCGAGGTAAAGACGAAAACCCAGCCCAGGTCATGGCCCACTTAGCAGCAACCATTAGATGCTATACTGCCCTAGACCCAGAGGGGCCAGAAGGCCGCCTTATTCTTAATATGCATTTTTATCACCCAATCCACTCCTGACATTAGGAAAAAACTTCAAAAATTAGAATCTGGCCTTCAAACCCAGCAGGAATTAATCAACCTTGCCTTCAAGGTGTACAATAATAGAGAGGAAGCAGCCAGACGGCAACGCATTTCGAGTTACAATTACTTGCCTCTGCTGTGAGACAAAACCCAGCCACACCTCCTGCATACAGGAACTTCAAAATGCCTAAGCCGCAGCAATCAGACACTCCTACAAGACTTCATCAGGATCTTGCTTCAAGTGCCAGAAATCTGGCCACTGGGCCAAGGAATGCCCACAGCCCAGGATTCCTCCCAAGCCATGTCCCATCTGTGCAGGCACCCACTGGAAATCAGACTGCCCAGCTCGCCCGACAGCCACTCCTGGAGCCCCTAAAGCTCTAGCCCAAGGCTCTCTGACTCCTTCCCAGATCTATTCGGCTTAGCGACTGAAGATTGACGCTGCCCGATCGCCTCGGAAGTCCCCTGGACCATCACAGAAGCCGAGCTTCGGGTAACTCTCACAGTGGAGGGTAAGTCCATCCCCTGTTTAATCGATACGGGGGCTACCCACTCCACGTTGCCTTCTTTTCAAGGGCCTGTTTCCCTTGCCCCCATAACTGTTGTGGGTATTGACGGCCAAGCTTCAAAACCCCTGAAAACTCCCCCACTCTGGTGCCAACTTGGACAACACTCTTTTATGCACTCTTTTTTAGTTATCCCCACCTGCCCACTTCCCTTATTAGGCCGAAATATTTTAACCAAATTATCTGCTTCCCTGACTATTCCTGGAGTACAGCTACATCTCATTGCTGCCCTTCTTCCCAATCCAAAGCCTCCTTTGTGTCCTCTAACATCCCCACAATATCACCCCTTACCACAAGACCTCCCTTCAGCTTAATCTCTCCCACTCTAGGTTCCCACGCCGCCCCTAATCCCACTTGAAGCAGCCCTGAGAAACATCGTCCATTCTCTCTCCATACCACCCCCCAAAAATTTTCGCCGCTCCAACACTTCAACACTATTTTGTTTTATTTGTCTTATTAATATCAGAAGGCAGGAATGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCCTGTGACTTGCACGTATACATCCAGATGGCCTGAAGTAACTGAAGATCCACAAAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAGACTCCCTCCCCCCACCCTTAAGAAGGTTCTTTGTAATTCTCCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGATTGTAATTTTTTATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTTCCTTCACTGAACTCTCTTTTCGGACTCAGCCCACCGGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGTATGAAAAAAGTCTCGCCCTGTTGCCCAGGCTGGAATGCAGTGGCACGATCTTGGCTCACTGCTACCTCCACTTCCTGGGTTCAAGTGATTCCCAAGTAGCTGGGATTACAGGTGTGTATTACCATGCCCAGCTAATTTTTGTATTTTTAGCAGATAAGGGGTTTCACCATGTTGGCCAGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACTTCGGCTACCCAAAGCATTGGGAGTACAGGGGTGAGCCACTATGCCCAGCCTCACATCATATTTCTAATCCCGAGACTGTAGAGCTGGTGTCTCTTTTTGGAAAGGATGTCAGTAGAGAAAATGGAGTTCCCCAAAATTACAGTTTCACATATTAGTAAAGTTTCTAAAATACAGTAATAATGTTGAGAGCTGACATAGGGACTAACTTAGTTTTTTTTTTTTTTTAGATTGTCACCTAACTTTGATTTTGCTAAATAAGGACATTAAAAGAAAACCAAAAAAGTCCACTATTGGCTATTGCCACTATTTGATTTTTTAAAAAATAAGCGTATTTTAGCATCTAAAAGTAGGAAGGACCTCAAATAAATGAGTCTTTGTTCTTGGCCAGGGAAACAGCGTTGTCAGCATTTGATAACTGTTTTTCTAGGGTATGTGCTGTTATTCAGTTAAAACCTTGCCTGGGGATGTTAGCATTGGTAAATACTTGTTGAATAAGCAAATGAAACTTAAGCTTCTATGTATAGAAACCTAAGTCACTTCACATTCTGATTAGCAGAGTAATTGAATATTCTTTTCAGTGTGTAGATCTATACCCAGAACCACAGAATATCGGAACTGTAAAAACCAACTGCATTAAATAGATGTGGTATGTGGCAGTGTACCAAGGTTGTGACTAGAACTCCGGTCTTGGAGTGTTCTATTATATCACACCAAGCTGGTCACCAGCCCATGTGTTGATCCTCCATTGTGATAGCAACAAAGAAAAGACTTCAGGACATTCTTTCCTTTACCCTAATCCTTCATCTTCAGTCTTATTTAGAAAAGCTTAATGTTAAAGATCTAGTTTATTCAAAACTAAAGATAAGGAGTATGAGAATTTCTATTTCGGAGTGTAAAGGAGGAGATGTTTCCTTGGCTTCTCTGAGCCTACAGGCCTTCCTTGCTCTTTAAGGAAGTAGAGAGAGAGAGGAAAGTAAAGTATGCTTTTGTTTTTTAAGGTTACTTTGCTGGGAGTAGTTTGCATGCCATTTGGTTTTCTTGGGTGGAATTAACTGACTTAAGTTTTAAGTAGTTGGGACTATTTAGAAACAATGCCTATCCAATGTTTGCCATAAAGGCAGAGGGTATTGGCTTTAGAAGTTAATTCTTCTCCAGGAGTGAAAATGAGCTGCTAAACCAGAAGCAGCAGAGCTAAAGAAAGTAATTTTCCACCTGGCCAGTGCATGATGTGAAAGGTAGACTAAAAGAATGAGAGGACCCATTTTCTGATGAAAGACTAAGCCATGTTGAAACAGCCCTGTTGAGGATTTTATTTTAAATCTATACATTCACAAAGGAGCTTTGTGTATGTCTTTCCCTATTTGTTGTTTGGACTAAGGGAGCCCCACCCAGTGCTTGTTCAGTAAGTTGTTGAAAGAAATCTGGATTTGAACAGTGGATTGAGGTTTCGAATATCCAGTGAACCAAAATATATCAGGGTTCCCCTGGCCAAGATGAGTGACCATTCTGAGGTGTTACGTATTTCTTGAATGGGGATTTTAGGAAAAGTTTCTGTATTTCTGTGCTCATTTTGTTGACCTCTGTATGTGCAAAATCTCTAAGGGGGTGTTTGGGCACTTAGATTTCTTGGATGCAGATTTGTTTGTATATGAAACAAATTTTAAATTGTTTCGTATACACTGGATTTAAAATAGTTTAGTTTACTAAAGTGTTTTAATGTTTTCATCTTAATTTTCAGTTCTTATAGTCTTTAGATTTAGGGAGGCTGTTGATGGCATCCACATATGCATTTTAATGTCATTTAAAATGTATTCTGCTGAATTTAACAATTTCTGACCTAAAACTTGACATTTTAATATTTAAGTCGGTAAAGCGCTGATTTAAACTGGATTTTAACTGGATGAAATTCTGATTTAATGAGTGTACTGACTGGATAAAATGCCAATGATTTAATTAACAAGCACGTTTACAGCATGCCCTATATATTAGTTAAAAGTGAAGCAATTGAATTAGGTACCATTTCAAAATGGTTGCTGTACCCACTCACCCTCTCTATCCTCCAATTAGGGTATATTTTGAAATGATTGCTTTTCCCTTTTCCTTGTGTAAAGAGCCTGAGGAAATTTTCTTCGGCCTTCATCATGAGAACCTGGTGGGGTTTCTGGAAGTAAAATTCATGAAAGTATAAGGGGCCCCCAAGACGGGACTCCAACAAGTTTTTAACTCTCAAGCTAGTCCACACTCAGCCACCAGTAAATTTATTGATTACCATTGAAGTGTTCCTACCAATTAC\t9\tPASS\tPRECISE;SVTYPE=INS;SVLEN=5362;END=10126;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.200;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:2:8:2",
+                "chr22\t13000\tSniffles2.INS.3S0\tT\tTGATAATCAAGAGAACGTCTCAGCACCGCGCCTGAGCGCTTAGTAGGTAGTGATCAAGAGAGAAGACCTC\t36\tGT\tIMPRECISE;SVTYPE=INS;SVLEN=69;END=13000;SUPPORT=2;COVERAGE=11,13,13,16,51;STRAND=+-;AF=0.154;STDEV_LEN=6.364;STDEV_POS=37.477;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:10:11:2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T13:26:19.039514387"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], false, true -stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ],
+                "snf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T12:18:29.154473769"
+    },
+    "homo_sapiens - [bam, bai], fasta, bed, true, true": {
+        "content": [
+            [
+                "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+            ],
+            "test.snf",
+            "test.vcf.gz.tbi",
+            [
+                "##fileformat=VCFv4.2",
+                "##source=Sniffles2_2.4"
+            ],
+            [
+                "##contig=<ID=chr22,length=40001>",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend; Translocation\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase-block, zero if none or not phased\">",
+                "##FORMAT=<ID=ID,Number=1,Type=String,Description=\"Individual sample SV ID for multi-sample output\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FILTER=<ID=GT,Description=\"Genotype filter\">",
+                "##FILTER=<ID=SUPPORT_MIN,Description=\"Minimum read support filter\">",
+                "##FILTER=<ID=STDEV_POS,Description=\"SV Breakpoint standard deviation filter\">",
+                "##FILTER=<ID=STDEV_LEN,Description=\"SV length standard deviation filter\">",
+                "##FILTER=<ID=COV_MIN,Description=\"Minimum coverage filter\">",
+                "##FILTER=<ID=COV_MIN_GT,Description=\"Minimum coverage filter (missing genotype)\">",
+                "##FILTER=<ID=COV_CHANGE,Description=\"Coverage change filter\">",
+                "##FILTER=<ID=COV_CHANGE_INS,Description=\"Coverage change filter for INS\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_US,Description=\"Coverage fractional change filter: upstream-start\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_SC,Description=\"Coverage fractional change filter: start-center\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_CE,Description=\"Coverage fractional change filter: center-end\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_ED,Description=\"Coverage fractional change filter: end-downstream\">",
+                "##FILTER=<ID=MOSAIC_AF,Description=\"Mosaic variant allele frequency filter\">",
+                "##FILTER=<ID=NOT_MOSAIC_AF,Description=\"Variant allele frequency filter for non-mosaic\">",
+                "##FILTER=<ID=ALN_NM,Description=\"Length adjusted mismatch filter\">",
+                "##FILTER=<ID=STRAND_BND,Description=\"Strand support filter for BNDs\">",
+                "##FILTER=<ID=STRAND,Description=\"Strand support filter for germline SVs\">",
+                "##FILTER=<ID=STRAND_MOSAIC,Description=\"Strand support filter for mosaic SVs\">",
+                "##FILTER=<ID=SVLEN_MIN,Description=\"SV length filter\">",
+                "##FILTER=<ID=SVLEN_MIN_MOSAIC,Description=\"SV length filter for mosaic SVs\">",
+                "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"Structural variation with precise breakpoints\">",
+                "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"Structural variation with imprecise breakpoints\">",
+                "##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description=\"Structural variation classified as putative mosaic\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of structural variation\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variation\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Mate chromsome for BND SVs\">",
+                "##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description=\"Number of reads supporting the structural variation\">",
+                "##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description=\"Number of reads supporting an INS/DEL SV (non-split events only)\">",
+                "##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description=\"Number of soft-clipped reads putatively supporting the long insertion SV\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of structural variation\">",
+                "##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description=\"Standard deviation of structural variation start position\">",
+                "##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description=\"Standard deviation of structural variation length\">",
+                "##INFO=<ID=COVERAGE,Number=.,Type=Float,Description=\"Coverages near upstream, start, center, end, downstream of structural variation\">",
+                "##INFO=<ID=STRAND,Number=1,Type=String,Description=\"Strands of supporting reads for structural variant\">",
+                "##INFO=<ID=AC,Number=.,Type=Integer,Description=\"Allele count, summed up over all samples\">",
+                "##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description=\"List of read support for all samples\">",
+                "##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description=\"Number of reads that support the generated insertion (INS) consensus sequence\">",
+                "##INFO=<ID=RNAMES,Number=.,Type=String,Description=\"Names of supporting reads (if enabled with --output-rnames)\">",
+                "##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">",
+                "##INFO=<ID=NM,Number=.,Type=Float,Description=\"Mean number of query alignment length adjusted mismatches of supporting reads\">",
+                "##INFO=<ID=PHASE,Number=.,Type=String,Description=\"Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE",
+                "chr22\t1\tSniffles2.INS.0S0\tA\tATTAGGCAAAGAGAATATACTCGACTCATTTTGCTATACAGGAAAAAAGTGCTTCCTTAGCTCATTTGGAAAGAGATTGAGATTAGAAAAGATGGTTAATTTGTATGTATTTATAGAAATAAATAGAATACAAAATGAGGCTTTTAAATTTTTTCCCACATGAAAATATGATTACTTTAATCATTACGTTTTACATTGTTAGTTTGCAGACAGGCATAATTAGGTCCTCAGTTGCAGAAATCACAGACATCTGAAGGCCAGCCCTTTAATTTGGCCACCCCTAGATTTCTCTGCTCCTTCCTTTGCTCCTCCTACTGCACAGTTTGAACTGATGCTGTTCTATATAAGGTACTTTTCCACCTACCTCATCTCTGACTACAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACCATGCCAACAATCAGGGCACCACCTAGCAGAGTCAGTGAAGGCCAAAATAAACAGTGGAAGATAGCCATTTGGTCATACTTTTTTATAAGAATGACATCTTCAGATTGGCTGGCTGGACTGTAGAAGCATGAAAAGGGGGTTCCATTTTTGTGATCGAAGAATTCTTTTATGTCCAGAGCACTGTTGAGCAAATCATTTCTATCTTGGTGGCACTTAGGTGTGTAAAAGCACTAGGAATATGGAAGAGGGAAAAAGATAAAGGCACTGTCACCAATACCAAATACTTAACAGTTTCTAATTATGAAATAGCTTCAGGCTGAAGTTATTAGTGGGCAGTTTCAATCTTAGAAGGTGGTAAAATATTACATAGCTCATGGGAAAGGGTTGATTGGAGGGCCACAGTGAAATGGCCATTTCCAGTCATTAAGCAAGGATGTGGAAGAGAATTCTTAGTTTATATGACATTGCAGGAGAGTCAGTGACCAATTTCATAAGGAATATGACTCCTCCCTACATGCAGGTTCTTGGACTCTTGGACAGTATGAATCCGTTTGTCCATTGAACAAAAATGTATTGAGCCTTACTATGAGCTTTCAACACCTAGTAGTGCCTCTGTGGTCTCTGTCTTGATCTCCTGTAGCAAAATATTACCCTGAAGAAAAGCACGTTGAGGCTTTTGCTCTAGACTCACAGACAGGGAGCCCCACCTGGACTTTGGTTCCTGGGAGACAGAACCAGTGGAGAAGGGAGCTCTGTCAGCTGGTGACTTTTTTAAAAAAGCTTGAGGTTTATTACCATATCCATTAGGTACTTGAGGTACTGTGCTAAAGGCCTACAAACTGTTTGAAATCTTAAAAATCATTGCATCCAAAATAGAAAACAAAAGTCATCAGATTGAAATTGTAGGACTAAAGACAATAAAGTGTAACATGTCAACTAATCTTAACACAACTCAACTTTTATAGTTAGGTATAAATATAAATTTTAAATGATATGAAAGACTATACTTTCAGGGATCATTTCTATAATTCGTTAAATTATATGAACCCATTGTGTAACTTATTAAAATAAAAATAATCTTTACATTTATTTGATAAGAAAAAATTACTCGCTTGATTCAAGGGAGACTGTGGTACACTGTGTAGCATATGTTATATGGCGCGGAGTGGAATCTCCAAAAGAAAGACTCCCCACAAATGACTACTCATTGGCTCAGCCTATAAATTCCAGACACCAAGTTGTGAAATTGGAATAATTTCTCTCCTTTCTATATACCCCATTTCTCCACCAAGAAGAAAGCTTCATTTATCCTGATTTGATCACTATAAAAATGTTCACTCCAAAAAAATAGATTTATCCCTAAAGACAGCCCTGGGTTATTTATGTACCCTGCTAGGGACAGTCTGGCAGGGAAGGGTTGCTGTCATAAGAACTCTTTAAACTTTACAATACCTTGGGATTTATCTGGACAGCCTCTTCATTATAATGTAGGAGAGCTTTCTGAGCTGAATGGGTGAGGTTCACAAACACCCGAAGACACGAGTACTTCCCGTGACCACGGCAGTGCACACCACAGGTGAAGGCACAGTCCAGCCAGTCGTCCATGATATCTGTGTGGATGGCAGTGCAGGTTGATTCTTCTCTCCGAATGCTTCAATTTGAAAAAAAAAAAAATGTTCTTCACTTACTAGAAAATTTCGTTCTACATTTTGGTGCGGTTATGAGCTTATGTACACAATTAGCTGGGATTACAGGCGCTCAGCTGCCATGTCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTGTTGGCCAGGCTCGTCTCCAACTCCTGACCTCAAGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCTGGCCCAAATACTATGTTTTATCAATTCTAAAGTGCACTTTAGTATTTACATTTTAATATAACTAAAATCAATATGTATTTTGCAATCAATGGCATCTTGCTATTATTTGAAAACATTTCTTTAATAGTCTGTAAAATAATGGAACATGCCCAGATGCAGTGGCTTGTGCCTGTAATCCCAGCACTTTGAAGGGTCAAGATAGGAGGATCGCTTGAGCCCAGGAGCTGGAGACCAGCCTGGCCAATATAGTGACAGAATAAATAAATAAGTAAATAAAATAATGGAAAATCTCACAAATGGTGATGTTTTAGGTTCGACAAAATACATTAACTAGCCCATTTAGTTTTCTGAAATTATTTTGATGTTATTGCTTACAATATTTGTTCTGTGGTACACAACCATAGGATTAATAATATTGATGAAAATAATAAAAGAATAATAAGCATGTATTGAGCTCTTCCTGTGTGAAGTTCTGGACAAATCCTCATAAAGCCTTAAAAGGCAGATACTAGGCTGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACGAGGTCAGGAGATTGAGACCATCCTGGCTAACATGATGAAACACGGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCTGAGGTTGCAGTGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGCGACAGAGCAAGACTCTGTCTTAAAAAAAAAAAAAAAAAAGAAAGAAACAGGCAGATACTAGCCCAGGCACGGTGGCTCATGCCTGTAATCCCACACCTTCGAAGGCCCAGGCGGGTGGATTATCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATTGTGAAACCCTGTCTCTACTAAAAATACAAAAATATTAGCCAGGTGTGGTGACAGGTGCCTGTAATTCCAGCTACTCAGGAGGCTAAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATTGTGCCACTTTACTCCAGCCTAGGTGACAGAGGAAGACTCTGTCTCAAAAAAAACAAACAAACAACAACAACAACATCAAAAAGAAACCTATAGTAATAAAATTGAAACAGAAGGAGGTTTGCAATCAAAATGACTGACTAGGAATGAAATAGGAAAACATAATAATTTGCATCTGCATAGGGAAGTCTGAGATTGGCTGATCTTGTTCTCTTCGAGGGGGAATACTAGTCCAGAACTTGGGGTGCCTGCCAAGAGGGGAGCAGCCACAGTAGGAAAGGGGGACTCTGGAATGCTAGGGTTCTGGGGTCTGTGGACACAGGAGGCAGAGGACATGTGTTAAGATGTTTTAAGAAATGAATGTTGAACTGGATATGAAAATATTTTTCAGCCGGGCGCAGTGGCTCACGTCTGTAATCCCAGTACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCCGTCTCTACTGAAAATACAAAAAGTTAGCCAGGCGTGGTGGCGGAGGCCTGTAATCCCAGTTACTCTGGCGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGACGGAGCTTGCAGTGAGCCGAGATTGCGCCTCTGCACTCTAGCCTGGGCGACAGAGGGAGACTCCATCTAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAATATTTTTCACTATAGAGAGGCATATGTCCCCTGAACTTGCCGGGATCCACCTTTCCTGCTGGTGCATTCTGTGAGTTAGAAGAAAACTTCCAAAGAGCCATTTTTTCCACCCTGTCTACTGTATAAAATTGCTTCTCAAACATGTGCTGCATTGCAGAGGATTACCATTGTTTTGCTAACCAGCGTCTGGTCTTTCTTATGTGGCGCTGCAATTACTAGTGTCAAACCCTGTTGGTAATACCCAGAGGATGGTGTCTGAAGTCTTTACTCAATATTCACATTGGCTGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTCGGAAGCAGAGGCAGGCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAAATTAGCCGGGTATGGTGGCGGGTGCCTGTAATCTCAGCTACTAGGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGATTGTGCCACTGTACTCCAGCCTGGGGGAAAATTCACATTTGTAGAGAGTTTAAATTCTTTTTTGATACGGAGTCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCAGGGTCTTGACTCACTACAACCTCTGCCTCCCAGGCTCAAGGGATTCTCCTGCTTTAGCCTCCTGAGTAGTTGGGATTACAGGCACCCACCAAAACACCTGGGCAATTTTTGTATTTTTATTAGAGACAGGGTTTCACCATGTTGTCCAGGCTGATCTGAAACTCCTGACCTCAGGTGATCTGCCTGCCCTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCCGGCCGAGAGTTTAAATTCTTAAATCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCGTCTCAGTATTTCTATTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCAATTCCAGGTAAACTTTGGCCTTTTATGAATTCTCCTGATCAGGCCAAACCTCAACCAAGTCCCTTCTTGATCTTCTCCTTCACCTCCTTCCCTCATTCACCCAACAATTAGCCTCCAGTCCACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAAGCCTCAGCTAAAGTTTACAATCCTACCTTTTCTACTGCCTTGAAATGCCCTAAGGTTCAGGGGCTTCATGGTTGCTGCTTCATGGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCCGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTCTACAGCTCTGCTGTCCCATTAACAGCACCTTTGGGGCCCCAGGGTTCCAGATTGGAAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCTTTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTCTACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAGAGGATCTTTAGCCTGCGGCGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAAGGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGATCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAATAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGAGGAAAGGATGGAAACTACTACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCTTCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGTTTTTGTAGATTGAAGTCTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCCAGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGAAATCCTTCCACCTCAGCCCCCCAAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGTTAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAAGTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGTATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGGCCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCAAATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCATCTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGCTATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGAAGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGGCCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCCCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGAAAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACAGCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAATATCTGAGACCTAGCATGCTAGGAGACCTTTATCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAAATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGATGTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCA\t44\tCOV_CHANGE_INS\tPRECISE;SVTYPE=INS;SVLEN=7407;END=0;SUPPORT=3;COVERAGE=0,0,0,0,8;STRAND=+-;STDEV_LEN=16.000;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t./.:0:0:0",
+                "chr22\t10115\tSniffles2.INS.1S0\tA\tAATGTGAAATTGCAAATAATTCACCTGAGAAATGAAAATTAATCTTCTTTGCTAAATGCCATAGAGATATTTTAAGTTGCTAATGTTACTTAGATGTTCATTAACTTAGTGAGTTACATTAAGTAGAGAAGATGCCTTTTTTTTTTTCTGTACGAAGTCTTGCTCTGTAGCCCAGTGTAGTGGTATGATCTCGGCTCACCACAACCTCCGCCTCCTGTATTCAAGCGACTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGATTACAGGTGTGCACCATCGCACCTAGCTAATTTTTTGTATTTTTAGCAGAGACAGCATTTCACCATGTTGGCCAGGCTGTTCTTGAACCCCCGACCTCAGGTAATCCACCCTCCTTAGCCTCCCAAAGTGCCAGGATTACAGGCGTGAGCCACTGCACCCTGCTGAGAAGATGCCTTTTGACAATGAAGTGGATTTGTATATTTATCTTTGGCTTAAAAAAACATGCACCACCAATTACACTTTCCTCAAGTTTAAATTTTTAATAATTAGGAAAATAAAGCATTTTCTTGTCTTATAGTGTTAGCTAGATTGTTTTTGTGTATTTTGTCATGAATAAAAAGCATAGCTATATAGTTACTGCTTTTACATTAACTATAAATATCTTAAAATTTTACTACCTAAAATCAGGAAACTTGAACTGAAGCTACTAATCTTAGAGTTGGAAAAGTAAATACATAGAGGTTTCCTGTTGTACAAATGTCAAGTGGCACAGTGAAATTTACATTCATTTGAAAGTTTTCCTAACTGTAAAAAGTATCAAATTACTTGATACTTTGGAGTAGTTCATCATCTTTATCAGAGGCACAGGTCTTAACCATTGGCAAGCCTCTGTCAGAATATGCACATATTAAAGATCTGATTATTTTTGTGTTAATGTTAAAAAATTTTTCTGAAGCTTTTATCTTATTTTTTCCATCCTTACACCGTAAATTCACATTACCAAGTTGGGAAGCCAAAGAAACATTCTACTCTACTCATGTTTTTTCACCAGTTCATGAAAGTTGATGTTAGAAATGGGTGTGGGTGTGGGGGATGGGGGTGGTTGTACAGAAGCAGCAGGTGGTAGGGATAGGATTTCTGAAGCACTATCCTTGGCCTTTTTTGAGTAAACTCTTTATACCCTGAGCCACTTTCTTTTCAGAGGGCAATTGCTATTATTAGAGAGCCACCTTAAGCATTATTGTTGTAGAAAAATTAGGCACAACCAGTGATTGTCATTACAAGGACCAGCAAAAATGGCTAGGTTGCTACTCTGTATTTGTAACGCCCTTCCCCCAACAAAATTTCTCCTTTTCATATCTGTGAATTAGAAATAAGTGATAGAAAACTGTACTGCATTACAATATATACCATTTAATAAAACAAGTTTATAGTTGAGAGCACTATTCATGCTTTTTGAAAGAATGCAAATTTGTAATTTTTATGATAGCAATTCTTAATAATTTATTGTCCAAGAGATTTGATAAAATTTTTGATAGTTATTGGTCTCTGGGACTCAATAGGCACTGGAATGTTTTAATTCAGTTGAAAAGTTGGTTCAGGATTGCTACCCTCTCTTACCTGTTAGGAGGTTGTTGTTTAACCTGACCTGAAATTCCCATGAATAAGAACCTGTTTTTTTTTTTTTTTTTCTTTGACAGAGTCTTGCTCTGTCGCCCAGGCTGCAGTGCAGTGGTGCGATCTTGGCTCGCTGCAAGTTCCGCCTCCCAGGTTCAAGCGATTCTCCTGTCTCAGCCTCCCAAGTAGCTGGAGTAGCTGGGACTGCAGGCACGTACCACCATGCCTGACTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCGCAATCTCTTGACCTCATGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCACCTGGCCCAGGGAATTTCTAATATTTGAGAAGATGTTATTTTTAGTCTATTATACAAATTTATATATTGTTTACTAATATATAAATTTACATATTGGTTACTAATATGTAAACACCAATTTACATATTGGTTACTAATATGTAAACTTGATAAACATGGATTTCCATGGAAATTTAAAAGTATCACAACAATTTGTTTTCCCATTCTGAAACTTGTGATTTATTACATTTTCCTACTATTTCAGTTAATTCCATAATGCCAGATTTGTTGTAAATTTGCCGAGTGACAAGCCACACTGCTTCCTCTCATTCCTCTATTCCACAAAACTGCAAAGTTTCCCAGACCACAGTCAGGTTTCTCTGGGTTGTCCACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTAAGTCACTTTAAGTTTATGACGGAGGGGCTTCGTGAAACTTCATTGACCTTCCAAGGTGAAAATTGGTCAGTTTTCAGTTATAAAGGACATTAAGGATGGGTGTGGTGGCTGATACATGTAATCCCAGCACTTTCGGGAGACTCAGTCAGGAGGATCACTTAATCCTCATTTAAAAGGAGTTTGAGACCAGCCTGGGCAACAAAGTGAGGCCTTGTCTCTACAAAAAAATTAGCTGGGTGTGGTGGTAGGCACTTGTAGTCCCAACTACTCTGGAGACTGAGCTGAGAGAAGATTGTGTGAGGCTTGGAGGTTGAGGCTGCAGTGAACGGACATCACACCACTACACTCTAGTCAGGTGACAGAGCAAGACTCTAAATAAATAGGAACATTAGATGGTCTCTCTGCACTCTTGCCTGGTGGGGACGTGTTAGATACCCTCGTTAGGTTGTGATTTAGTTTTTAATCTGTGAGATGTTTGGGTCAAACAATTTTTAGCTGCCATGGAATAAACTTTCCAGTCAACGTGTGAGTTTGTGTTTGCCTTTACTTTTTTTTTTTTCTATATTGTTTTGGTCTATTTTTATCTTTTAATTTCAGAAAGCTGATTAATCTCTTCCTTTTCTCTTTAAAAATTTTCTTTATCATGTTTGTGCTACAGTGGTTATTTTGAGAACTTGTTGGCAGGATAAGTTGCAAAAGTTATGAAGTAGAATAGGGATGATTTCTGTTTTTGTTTTTTTTTTTTTCAGACAGAGTCTCACTCTCTTGCCTAGGCTGGAGTGCAGTGGCGTGATCCTGGCTCACTGCAGCCGCCGCCCTCCGGATTCAAGTGATTTGCCTGGCTCAGCCTCCCAAAAAGCTGGGATTACAGGTGCATGCCACCACACCCAGCTAATTTTTGTGTTTTTAGTAGAGATGGGTGTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCCGCACTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCATGCCTGGCTGAGATTATTTCTTTTTTTATTATAGCCATTGCTTGTAGATATATGCTGGTGGTTATCTGTAAAAATGTAATAGAAAGGCCGGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACAAGGTCAGGAGTGGGAGACCAGCCTGGCCAATATGGTAAAACCCCGTCTCTACCAAAAATACAAAAATTAGCTGGGCATAGTGGCGGGCACCTATAGTCCCAGTGACTCGGGAAGCTGAGGCAGGACAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGATCGTGCTATTATTGCACACCAGCCTGGGCGACAGAGTGAGACTCCGTCTCAAAAAAGAAAAAAGTAATAGACCAATCTTGAATTTATAATTGGAAGTGTTATTTCTTTATTTGCAGAATTTATTTATTTGTGACGCAGCTGTTGCTACCTCGCCTTTTCTTTTGTTGAGCTTAATCTCATGTCAAGTCATTCAACCAACTCAAAAGCGATGAAGACATTATTGAATCAACCTGAACTAAATCAGACCTAGGCTTCTTAAAATATACAGCTTAATGCTTCCAAATGATTTAGAAAACTAAAAAACCTAGCTACGCTGTAGGACACACAGTGGCCAATAAAAACAGGACCCCCAAACTGGCCAGTGGACCACTGCAACCACTATTTACTTCCTCCGTGTTTAGGAATGTTCAACGCTCCAAGCCCCATAGGCTGATTCAAGAAGATAAAGTGAGACTCAAGGAATTTCGAAGTGGAACAATACACCAAAGCCTTAAACCTGAAATGACTCTCCTTTTCTGGGGGTGAGGGAAGAAAAAGAAAAAGTTTCTAGGGCTCTCGGGGTGGCCTGGATGCCAGGGTCCCAGAAGTGGCCTTTTCTAGCTCCTGTAACTAAACCTGGCGGAAAACTCCCCGCCTGCTCACTCCACCCCCACCCGCCCAAGAATGCGTCTTCCCGTCTTCGGTGGCCCTACCCAGAATCCCAAAATGTGGGTTCCAACCCGGGCCCTGAATGTCTTCTCAAATCCCCGGGACCCAGGTTCCGGTGCGTGCCTTGCGTGCCGGGTCTTGCCCCTCGGGCGGTACCACCCAGGCAGCCCTAAATCCAGCCTCCCGGGCCCCCAGCAGCGCCCTCCGCCCCTCCACTATCCGGTCCGGCTCGAAGTCGGGGCCAAATCCAGAGACAAGAGGGCTGTGCCTGAAACTGAGCAGTTTCACCACTCGGCACTCCTGGCGGAAACTTCCCTTTAAAAAAAAAAAAAAAGAAAAGAAAGAAAAGCAACAGCACTTTTGGGCTAGCATTTCAATCCTTCCTGCCCTTTAGAGTTCCCAGTTCTGCTTCCAGCTGGCTTTGGGTGTTCCACTAGAATTGAGTTGTAAAGATATTCTTTAAGTGTTTATAGAACATTAAGACTTAAAAAAAATCTTTAAAATTAGAGGAGGGAAGCCACTGATCGCACACATCCAGGAAATGCAGCCCCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGACTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCGGTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGATCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAACTTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCCGCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTTCGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGATTCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGAGCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGGAAGCGCAGGAGCCGGCTGGGGGAGGGGGCGCCCTAGAGAAGCGGCTAGAAAGCTGAGACGGGGAACTGAGGTCATCCTGGGGGGGACAAGACAATGAGAGCCGGGCGCCTTGGGGGCGGCGCGGGAGCCTCCGCAGGACCAGGCGGGCGCCCCCTTTACCTGCGGCTCCGGCGCCTCGGCCGTTTCCTCGCGCGGCGGCGGCCGGGACTGAGCTGACACCACTCAGCCGGCGGGGTTTGAATGAGGAGGAGCGGGCGCGGAGGGGAGGGGGCGGGGAGGGAGGGAGGGAGGCGTCGCGGAGTTTCTCTCGGCCTTTTGTGCCATCCGCCGAGGCGCCTTGAGTATAAATCCAGATAGTGCAGTTTTTGTTGTGCTTGTGCTGATCAACTTTATGGTGTGATTAAATACGATTTTTTTTATTACGCTCTTGAAATTGTACTCTTGAGGTTGCAGAATGGCAATTAGATGGCAGTCGCTGATAGCCATGTAGAAGTTTTGATGAACATGCAAGTTAATTTTAATTTCTGATCAGTTACGGTTAGTGACTGTGGCCAAACATGTGCGTACTGATTCTACATGTGCTAATTCCGTGACGTTTATTCACCAGCTATGTGTCCCGTGCCTAATCCTGTGTCAGGCACCTTGTTCCAGGCATTGGGGGCAGCAGTGGACAAGGCAACAGAGTCTCCATCCTGAGGTGTTACTTTTAGAAAAAGATAGTTACAAGCAAATAAACAGGATGGTTTTAGATCTGGACAGAGGTTTTCAGAGGAAGTCATCCTTGAGCTGTCACAATGCTTTGGGGAGGGGTGTGCTGGGTAATCAGGGATGGCACATTTGGGGTGCCTAAGGATTGCTGTGGCCCTGGGAGCCTAGGACAGTTGGTCACAATTGACTTATTAGAGTCAGTCTCAGAAGCTTTCCTGGAAGTAGAATTGCTGCTGTTTTGCCAGGAGGGTTTCCTTCCCCATCTGACCACACAAGAAGACCCCTGCCCACAAATGCCTACCACTCCCAGGTCTCCCAGGCTGTTCACCCTCCCAGGCAAAGTGGAAGCTTCCTCTGTCCTAAGATCGTTTCCCACTGAACCTCCTTCATTTTCCTTCACTGCAGAGAAATAATCCTACAAGGTCTTGTGTGGAGAGTGATGGTACCTTCTTTAACCCAGATAATTGAGAATTGGAACCAAAACATCTGTGTATTAATAAATATTTTCAGTAACTAGGTTATGCTATTTCCCTGAGTGGGAAATAACACTCCATCATGTTTCTTTTTTTGGGGGGCAAGGGGGAGTCAAAGTTGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCGTGACTTGCACATATACATCCAGATGGCCTGAAGTAATTGAAGATCCACAGAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAATCTCCCCCACCCTTAAGAAGGTTCTTTGGAGTCTCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGACTGTAATTTTCCATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTCCCTTCACTTGACTCTCTTTTCAGACTCAGCCCACCTGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACGAAGCCTGTTTGGTGGTCTCTTCACACGGATGCGCATGAAATTTGGTGCCGTGACTTGGATCGGGGGACCTCCCTTAGGAGATCAATCCCCTGTCCTCCTGCTCTTTGCTCCGTGAGAAAGATCCACCTACGACCTCAGGTCCTCAGACCGACCAGCCCAAGAAACATCTCACCAATTTCAAATCTGGTAAGCGGCCTCTTTTTACTCTCTTCTCCATTCCTCCTCCTTCTCCCTTAGCTTCTCCAACCTCCCTCACTATCCCTCAACCTCTTTCTCCTTTCAATCTTGGCGCCACACTTCACCGCTTTTCTGGGGCAGGGGCAAGTACCCCTCAACCCCTTCCCCTTCACACTTAGTGGCAAGTCCCGCTTTCCTGGGCAGGGGCAAGTACCCCTCAACGCCTTCTCCTTCACCCTTAGTGGCAAGTCCCGCTTTTCTAGGGGGGCAAGAACCCCCAAACCCCTTCCATCTGTGTCTCTACGCTCTCTTCTGTGGGTTTGCTTCCTTCACTATGGAACCTTCCACCCTCCATTCCTCCTTCTTCTCCCTTAGCCTGTGTGCTCAAAAAGTTAAAACCTCTTCAACTCACACCTGACCTAAAACCTAAATGCCTTATTTTCTTCTGCAACACCGCATATCTTGCTTGGCCCCAATACAAACTTGACAATGTCTCTAAATGGCCGGAAAATGGCACTTTGATTTCCCCACTGACAAACACCTAAATAATTTTTGTCGAAAAATGGGCAAATGGTCTGAGGTGCCTTACGTCCAGGCATTTTTCACACTTCGTTCCCTCCCTAGTCTCTGTTCCCAATGCGATTCCTCCCAGATCCTCCTCCTTTCCTCTCCTGTCCCCTCGGTCCCAACCCCAAGCGTCGCTGAGTCTTCCCAGTCTTCCTTTTCTACAGACCCATCTGACCTTTCCCCTCCTCCCCAAGCTGCTTGTCGCCAGACCGAGCTAAGTCCCAAGTACCTCCCTCAACTCTCCACTCCTCCACCCTATAATCCTTCTATCACCTCCCCTCCTCACACCTGGTCCGGCTTACAGTTTAGTTCCGCGACTAGCGCTTCCCCACCTGCCCAACAATTTCCTCTTAGAGAAAGTGGCTGGAGCTGAAGGCATAGTCAAGGGACATGTACTTTTTTCTCTATCAGACCTCTCTCAGATCAGTCAATGTTTAGGCTCTTTCTCATCAGACCCCACTAAATATATACAGGAATTCCAATATCTAACTCTGTCCTACAACTTAACCTGGAGTGACTTAAATGTCATCCTGACTTCTACTCTCTCCCCAATATGAACGGGAAAGTTTTTTCTCTAGCCCAATCTCGTGCTGATAACCGCCGGCTTCATGAGCCAGACCTCCAGGAAGGCATTAGAGCAGTTCCCCGAGAGGATCCCCAATGGAACTATCAGGCAGATTCCCCAGGTACAGCTAGGCGAGATTACATGGTTTCCTGCCTAGTTGAAGGGCTTAAAAAAGCAGCTTACAAAGCTGTTAATTATGACAAGCTTAAAGAAACTACCCGAGGTAAAGACGAAAACCCAGCCCAGGTCATGGCCCACTTAGCAGCAACCATTAGATGCTATACTGCCCTAGACCCAGAGGGGCCAGAAGGCCGCCTTATTCTTAATATGCATTTTTATCACCCAATCCACTCCTGACATTAGGAAAAAACTTCAAAAATTAGAATCTGGCCTTCAAACCCAGCAGGAATTAATCAACCTTGCCTTCAAGGTGTACAATAATAGAGAGGAAGCAGCCAGACGGCAACGCATTTCGAGTTACAATTACTTGCCTCTGCTGTGAGACAAAACCCAGCCACACCTCCTGCATACAGGAACTTCAAAATGCCTAAGCCGCAGCAATCAGACACTCCTACAAGACTTCATCAGGATCTTGCTTCAAGTGCCAGAAATCTGGCCACTGGGCCAAGGAATGCCCACAGCCCAGGATTCCTCCCAAGCCATGTCCCATCTGTGCAGGCACCCACTGGAAATCAGACTGCCCAGCTCGCCCGACAGCCACTCCTGGAGCCCCTAAAGCTCTAGCCCAAGGCTCTCTGACTCCTTCCCAGATCTATTCGGCTTAGCGACTGAAGATTGACGCTGCCCGATCGCCTCGGAAGTCCCCTGGACCATCACAGAAGCCGAGCTTCGGGTAACTCTCACAGTGGAGGGTAAGTCCATCCCCTGTTTAATCGATACGGGGGCTACCCACTCCACGTTGCCTTCTTTTCAAGGGCCTGTTTCCCTTGCCCCCATAACTGTTGTGGGTATTGACGGCCAAGCTTCAAAACCCCTGAAAACTCCCCCACTCTGGTGCCAACTTGGACAACACTCTTTTATGCACTCTTTTTTAGTTATCCCCACCTGCCCACTTCCCTTATTAGGCCGAAATATTTTAACCAAATTATCTGCTTCCCTGACTATTCCTGGAGTACAGCTACATCTCATTGCTGCCCTTCTTCCCAATCCAAAGCCTCCTTTGTGTCCTCTAACATCCCCACAATATCACCCCTTACCACAAGACCTCCCTTCAGCTTAATCTCTCCCACTCTAGGTTCCCACGCCGCCCCTAATCCCACTTGAAGCAGCCCTGAGAAACATCGTCCATTCTCTCTCCATACCACCCCCCAAAAATTTTCGCCGCTCCAACACTTCAACACTATTTTGTTTTATTTGTCTTATTAATATCAGAAGGCAGGAATGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCCTGTGACTTGCACGTATACATCCAGATGGCCTGAAGTAACTGAAGATCCACAAAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAGACTCCCTCCCCCCACCCTTAAGAAGGTTCTTTGTAATTCTCCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGATTGTAATTTTTTATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTTCCTTCACTGAACTCTCTTTTCGGACTCAGCCCACCGGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGTATGAAAAAAGTCTCGCCCTGTTGCCCAGGCTGGAATGCAGTGGCACGATCTTGGCTCACTGCTACCTCCACTTCCTGGGTTCAAGTGATTCCCAAGTAGCTGGGATTACAGGTGTGTATTACCATGCCCAGCTAATTTTTGTATTTTTAGCAGATAAGGGGTTTCACCATGTTGGCCAGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACTTCGGCTACCCAAAGCATTGGGAGTACAGGGGTGAGCCACTATGCCCAGCCTCACATCATATTTCTAATCCCGAGACTGTAGAGCTGGTGTCTCTTTTTGGAAAGGATGTCAGTAGAGAAAATGGAGTTCCCCAAAATTACAGTTTCACATATTAGTAAAGTTTCTAAAATACAGTAATAATGTTGAGAGCTGACATAGGGACTAACTTAGTTTTTTTTTTTTTTTAGATTGTCACCTAACTTTGATTTTGCTAAATAAGGACATTAAAAGAAAACCAAAAAAGTCCACTATTGGCTATTGCCACTATTTGATTTTTTAAAAAATAAGCGTATTTTAGCATCTAAAAGTAGGAAGGACCTCAAATAAATGAGTCTTTGTTCTTGGCCAGGGAAACAGCGTTGTCAGCATTTGATAACTGTTTTTCTAGGGTATGTGCTGTTATTCAGTTAAAACCTTGCCTGGGGATGTTAGCATTGGTAAATACTTGTTGAATAAGCAAATGAAACTTAAGCTTCTATGTATAGAAACCTAAGTCACTTCACATTCTGATTAGCAGAGTAATTGAATATTCTTTTCAGTGTGTAGATCTATACCCAGAACCACAGAATATCGGAACTGTAAAAACCAACTGCATTAAATAGATGTGGTATGTGGCAGTGTACCAAGGTTGTGACTAGAACTCCGGTCTTGGAGTGTTCTATTATATCACACCAAGCTGGTCACCAGCCCATGTGTTGATCCTCCATTGTGATAGCAACAAAGAAAAGACTTCAGGACATTCTTTCCTTTACCCTAATCCTTCATCTTCAGTCTTATTTAGAAAAGCTTAATGTTAAAGATCTAGTTTATTCAAAACTAAAGATAAGGAGTATGAGAATTTCTATTTCGGAGTGTAAAGGAGGAGATGTTTCCTTGGCTTCTCTGAGCCTACAGGCCTTCCTTGCTCTTTAAGGAAGTAGAGAGAGAGAGGAAAGTAAAGTATGCTTTTGTTTTTTAAGGTTACTTTGCTGGGAGTAGTTTGCATGCCATTTGGTTTTCTTGGGTGGAATTAACTGACTTAAGTTTTAAGTAGTTGGGACTATTTAGAAACAATGCCTATCCAATGTTTGCCATAAAGGCAGAGGGTATTGGCTTTAGAAGTTAATTCTTCTCCAGGAGTGAAAATGAGCTGCTAAACCAGAAGCAGCAGAGCTAAAGAAAGTAATTTTCCACCTGGCCAGTGCATGATGTGAAAGGTAGACTAAAAGAATGAGAGGACCCATTTTCTGATGAAAGACTAAGCCATGTTGAAACAGCCCTGTTGAGGATTTTATTTTAAATCTATACATTCACAAAGGAGCTTTGTGTATGTCTTTCCCTATTTGTTGTTTGGACTAAGGGAGCCCCACCCAGTGCTTGTTCAGTAAGTTGTTGAAAGAAATCTGGATTTGAACAGTGGATTGAGGTTTCGAATATCCAGTGAACCAAAATATATCAGGGTTCCCCTGGCCAAGATGAGTGACCATTCTGAGGTGTTACGTATTTCTTGAATGGGGATTTTAGGAAAAGTTTCTGTATTTCTGTGCTCATTTTGTTGACCTCTGTATGTGCAAAATCTCTAAGGGGGTGTTTGGGCACTTAGATTTCTTGGATGCAGATTTGTTTGTATATGAAACAAATTTTAAATTGTTTCGTATACACTGGATTTAAAATAGTTTAGTTTACTAAAGTGTTTTAATGTTTTCATCTTAATTTTCAGTTCTTATAGTCTTTAGATTTAGGGAGGCTGTTGATGGCATCCACATATGCATTTTAATGTCATTTAAAATGTATTCTGCTGAATTTAACAATTTCTGACCTAAAACTTGACATTTTAATATTTAAGTCGGTAAAGCGCTGATTTAAACTGGATTTTAACTGGATGAAATTCTGATTTAATGAGTGTACTGACTGGATAAAATGCCAATGATTTAATTAACAAGCACGTTTACAGCATGCCCTATATATTAGTTAAAAGTGAAGCAATTGAATTAGGTACCATTTCAAAATGGTTGCTGTACCCACTCACCCTCTCTATCCTCCAATTAGGGTATATTTTGAAATGATTGCTTTTCCCTTTTCCTTGTGTAAAGAGCCTGAGGAAATTTTCTTCGGCCTTCATCATGAGAACCTGGTGGGGTTTCTGGAAGTAAAATTCATGAAAGTATAAGGGGCCCCCAAGACGGGACTCCAACAAGTTTTTAACTCTCAAGCTAGTCCACACTCAGCCACCAGTAAATTTATTGATTACCATTGAAGTGTTCCTACCAATTAC\t7\tPASS\tPRECISE;SVTYPE=INS;SVLEN=12815;END=10115;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.300;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/1:10:7:3",
+                "chr22\t13000\tSniffles2.INS.2S0\tT\tTGATAATCAAGAGAACGTCTCAGCACCGCGCCTGAGCGCTTAGTAGGTAGTGATCAAGAGAGAAGACCTC\t36\tGT\tIMPRECISE;SVTYPE=INS;SVLEN=69;END=13000;SUPPORT=2;COVERAGE=11,13,13,16,51;STRAND=+-;AF=0.154;STDEV_LEN=6.364;STDEV_POS=37.477;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:10:11:2",
+                "chr22\t13433\tSniffles2.INS.4S0\tC\tCTGGAAGATGCTGTGGTGAGTCAGTGAGTGTGAAGGCATAGGACCTTACTGTACACTACTGTAGACTTTATAAACACCATATGCTTAGGCTACACCAAAAATTTTTATCTCCTCTGATAACAATGCCTTCTTCTTCCAGAATACTTCCTGAAGGACCTGCCTGAGGCTGTTTTATAGTTAACTACTTT\t36\tGT\tPRECISE;SVTYPE=INS;SVLEN=187;END=13433;SUPPORT=2;COVERAGE=13,15,15,51,30;STRAND=+-;AF=0.133;STDEV_LEN=0.707;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:16:13:2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T13:26:58.425668806"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], true, false -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ],
+                "snf": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T12:18:17.116928744"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], true, true -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ],
+                "snf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.snf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T12:12:36.161185999"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], false, true": {
+        "content": [
+            [
+                "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+            ],
+            "test.snf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T12:14:02.409838384"
+    },
+    "homo_sapiens - [bam, bai], fasta, [], true, true": {
+        "content": [
+            [
+                "versions.yml:md5,0786af72683ced7f193b290fad51e914"
+            ],
+            "test.snf",
+            "test.vcf.gz.tbi",
+            [
+                "##fileformat=VCFv4.2",
+                "##source=Sniffles2_2.4"
+            ],
+            [
+                "##contig=<ID=chr22,length=40001>",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INV,Description=\"Inversion\">",
+                "##ALT=<ID=BND,Description=\"Breakend; Translocation\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase-block, zero if none or not phased\">",
+                "##FORMAT=<ID=ID,Number=1,Type=String,Description=\"Individual sample SV ID for multi-sample output\">",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FILTER=<ID=GT,Description=\"Genotype filter\">",
+                "##FILTER=<ID=SUPPORT_MIN,Description=\"Minimum read support filter\">",
+                "##FILTER=<ID=STDEV_POS,Description=\"SV Breakpoint standard deviation filter\">",
+                "##FILTER=<ID=STDEV_LEN,Description=\"SV length standard deviation filter\">",
+                "##FILTER=<ID=COV_MIN,Description=\"Minimum coverage filter\">",
+                "##FILTER=<ID=COV_MIN_GT,Description=\"Minimum coverage filter (missing genotype)\">",
+                "##FILTER=<ID=COV_CHANGE,Description=\"Coverage change filter\">",
+                "##FILTER=<ID=COV_CHANGE_INS,Description=\"Coverage change filter for INS\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_US,Description=\"Coverage fractional change filter: upstream-start\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_SC,Description=\"Coverage fractional change filter: start-center\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_CE,Description=\"Coverage fractional change filter: center-end\">",
+                "##FILTER=<ID=COV_CHANGE_FRAC_ED,Description=\"Coverage fractional change filter: end-downstream\">",
+                "##FILTER=<ID=MOSAIC_AF,Description=\"Mosaic variant allele frequency filter\">",
+                "##FILTER=<ID=NOT_MOSAIC_AF,Description=\"Variant allele frequency filter for non-mosaic\">",
+                "##FILTER=<ID=ALN_NM,Description=\"Length adjusted mismatch filter\">",
+                "##FILTER=<ID=STRAND_BND,Description=\"Strand support filter for BNDs\">",
+                "##FILTER=<ID=STRAND,Description=\"Strand support filter for germline SVs\">",
+                "##FILTER=<ID=STRAND_MOSAIC,Description=\"Strand support filter for mosaic SVs\">",
+                "##FILTER=<ID=SVLEN_MIN,Description=\"SV length filter\">",
+                "##FILTER=<ID=SVLEN_MIN_MOSAIC,Description=\"SV length filter for mosaic SVs\">",
+                "##INFO=<ID=PRECISE,Number=0,Type=Flag,Description=\"Structural variation with precise breakpoints\">",
+                "##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=\"Structural variation with imprecise breakpoints\">",
+                "##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description=\"Structural variation classified as putative mosaic\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of structural variation\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variation\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Mate chromsome for BND SVs\">",
+                "##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description=\"Number of reads supporting the structural variation\">",
+                "##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description=\"Number of reads supporting an INS/DEL SV (non-split events only)\">",
+                "##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description=\"Number of soft-clipped reads putatively supporting the long insertion SV\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of structural variation\">",
+                "##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description=\"Standard deviation of structural variation start position\">",
+                "##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description=\"Standard deviation of structural variation length\">",
+                "##INFO=<ID=COVERAGE,Number=.,Type=Float,Description=\"Coverages near upstream, start, center, end, downstream of structural variation\">",
+                "##INFO=<ID=STRAND,Number=1,Type=String,Description=\"Strands of supporting reads for structural variant\">",
+                "##INFO=<ID=AC,Number=.,Type=Integer,Description=\"Allele count, summed up over all samples\">",
+                "##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description=\"List of read support for all samples\">",
+                "##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description=\"Number of reads that support the generated insertion (INS) consensus sequence\">",
+                "##INFO=<ID=RNAMES,Number=.,Type=String,Description=\"Names of supporting reads (if enabled with --output-rnames)\">",
+                "##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">",
+                "##INFO=<ID=NM,Number=.,Type=Float,Description=\"Mean number of query alignment length adjusted mismatches of supporting reads\">",
+                "##INFO=<ID=PHASE,Number=.,Type=String,Description=\"Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE",
+                "chr22\t1\tSniffles2.INS.0S0\tA\tATTAGGCAAAGAGAATATACTCGACTCATTTTGCTATACAGGAAAAAAGTGCTTCCTTAGCTCATTTGGAAAGAGATTGAGATTAGAAAAGATGGTTAATTTGTATGTATTTATAGAAATAAATAGAATACAAAATGAGGCTTTTAAATTTTTTCCCACATGAAAATATGATTACTTTAATCATTACGTTTTACATTGTTAGTTTGCAGACAGGCATAATTAGGTCCTCAGTTGCAGAAATCACAGACATCTGAAGGCCAGCCCTTTAATTTGGCCACCCCTAGATTTCTCTGCTCCTTCCTTTGCTCCTCCTACTGCACAGTTTGAACTGATGCTGTTCTATATAAGGTACTTTTCCACCTACCTCATCTCTGACTACAGTGCTATATTTTTCACACAGTAAGGACAGGTGTTGTGTTAATCTCACCATGCCAACAATCAGGGCACCACCTAGCAGAGTCAGTGAAGGCCAAAATAAACAGTGGAAGATAGCCATTTGGTCATACTTTTTTATAAGAATGACATCTTCAGATTGGCTGGCTGGACTGTAGAAGCATGAAAAGGGGGTTCCATTTTTGTGATCGAAGAATTCTTTTATGTCCAGAGCACTGTTGAGCAAATCATTTCTATCTTGGTGGCACTTAGGTGTGTAAAAGCACTAGGAATATGGAAGAGGGAAAAAGATAAAGGCACTGTCACCAATACCAAATACTTAACAGTTTCTAATTATGAAATAGCTTCAGGCTGAAGTTATTAGTGGGCAGTTTCAATCTTAGAAGGTGGTAAAATATTACATAGCTCATGGGAAAGGGTTGATTGGAGGGCCACAGTGAAATGGCCATTTCCAGTCATTAAGCAAGGATGTGGAAGAGAATTCTTAGTTTATATGACATTGCAGGAGAGTCAGTGACCAATTTCATAAGGAATATGACTCCTCCCTACATGCAGGTTCTTGGACTCTTGGACAGTATGAATCCGTTTGTCCATTGAACAAAAATGTATTGAGCCTTACTATGAGCTTTCAACACCTAGTAGTGCCTCTGTGGTCTCTGTCTTGATCTCCTGTAGCAAAATATTACCCTGAAGAAAAGCACGTTGAGGCTTTTGCTCTAGACTCACAGACAGGGAGCCCCACCTGGACTTTGGTTCCTGGGAGACAGAACCAGTGGAGAAGGGAGCTCTGTCAGCTGGTGACTTTTTTAAAAAAGCTTGAGGTTTATTACCATATCCATTAGGTACTTGAGGTACTGTGCTAAAGGCCTACAAACTGTTTGAAATCTTAAAAATCATTGCATCCAAAATAGAAAACAAAAGTCATCAGATTGAAATTGTAGGACTAAAGACAATAAAGTGTAACATGTCAACTAATCTTAACACAACTCAACTTTTATAGTTAGGTATAAATATAAATTTTAAATGATATGAAAGACTATACTTTCAGGGATCATTTCTATAATTCGTTAAATTATATGAACCCATTGTGTAACTTATTAAAATAAAAATAATCTTTACATTTATTTGATAAGAAAAAATTACTCGCTTGATTCAAGGGAGACTGTGGTACACTGTGTAGCATATGTTATATGGCGCGGAGTGGAATCTCCAAAAGAAAGACTCCCCACAAATGACTACTCATTGGCTCAGCCTATAAATTCCAGACACCAAGTTGTGAAATTGGAATAATTTCTCTCCTTTCTATATACCCCATTTCTCCACCAAGAAGAAAGCTTCATTTATCCTGATTTGATCACTATAAAAATGTTCACTCCAAAAAAATAGATTTATCCCTAAAGACAGCCCTGGGTTATTTATGTACCCTGCTAGGGACAGTCTGGCAGGGAAGGGTTGCTGTCATAAGAACTCTTTAAACTTTACAATACCTTGGGATTTATCTGGACAGCCTCTTCATTATAATGTAGGAGAGCTTTCTGAGCTGAATGGGTGAGGTTCACAAACACCCGAAGACACGAGTACTTCCCGTGACCACGGCAGTGCACACCACAGGTGAAGGCACAGTCCAGCCAGTCGTCCATGATATCTGTGTGGATGGCAGTGCAGGTTGATTCTTCTCTCCGAATGCTTCAATTTGAAAAAAAAAAAAATGTTCTTCACTTACTAGAAAATTTCGTTCTACATTTTGGTGCGGTTATGAGCTTATGTACACAATTAGCTGGGATTACAGGCGCTCAGCTGCCATGTCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTGTTGGCCAGGCTCGTCTCCAACTCCTGACCTCAAGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCTGGCCCAAATACTATGTTTTATCAATTCTAAAGTGCACTTTAGTATTTACATTTTAATATAACTAAAATCAATATGTATTTTGCAATCAATGGCATCTTGCTATTATTTGAAAACATTTCTTTAATAGTCTGTAAAATAATGGAACATGCCCAGATGCAGTGGCTTGTGCCTGTAATCCCAGCACTTTGAAGGGTCAAGATAGGAGGATCGCTTGAGCCCAGGAGCTGGAGACCAGCCTGGCCAATATAGTGACAGAATAAATAAATAAGTAAATAAAATAATGGAAAATCTCACAAATGGTGATGTTTTAGGTTCGACAAAATACATTAACTAGCCCATTTAGTTTTCTGAAATTATTTTGATGTTATTGCTTACAATATTTGTTCTGTGGTACACAACCATAGGATTAATAATATTGATGAAAATAATAAAAGAATAATAAGCATGTATTGAGCTCTTCCTGTGTGAAGTTCTGGACAAATCCTCATAAAGCCTTAAAAGGCAGATACTAGGCTGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACGAGGTCAGGAGATTGAGACCATCCTGGCTAACATGATGAAACACGGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCTGAGGTTGCAGTGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGCGACAGAGCAAGACTCTGTCTTAAAAAAAAAAAAAAAAAAGAAAGAAACAGGCAGATACTAGCCCAGGCACGGTGGCTCATGCCTGTAATCCCACACCTTCGAAGGCCCAGGCGGGTGGATTATCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATTGTGAAACCCTGTCTCTACTAAAAATACAAAAATATTAGCCAGGTGTGGTGACAGGTGCCTGTAATTCCAGCTACTCAGGAGGCTAAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATTGTGCCACTTTACTCCAGCCTAGGTGACAGAGGAAGACTCTGTCTCAAAAAAAACAAACAAACAACAACAACAACATCAAAAAGAAACCTATAGTAATAAAATTGAAACAGAAGGAGGTTTGCAATCAAAATGACTGACTAGGAATGAAATAGGAAAACATAATAATTTGCATCTGCATAGGGAAGTCTGAGATTGGCTGATCTTGTTCTCTTCGAGGGGGAATACTAGTCCAGAACTTGGGGTGCCTGCCAAGAGGGGAGCAGCCACAGTAGGAAAGGGGGACTCTGGAATGCTAGGGTTCTGGGGTCTGTGGACACAGGAGGCAGAGGACATGTGTTAAGATGTTTTAAGAAATGAATGTTGAACTGGATATGAAAATATTTTTCAGCCGGGCGCAGTGGCTCACGTCTGTAATCCCAGTACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCCGTCTCTACTGAAAATACAAAAAGTTAGCCAGGCGTGGTGGCGGAGGCCTGTAATCCCAGTTACTCTGGCGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGACGGAGCTTGCAGTGAGCCGAGATTGCGCCTCTGCACTCTAGCCTGGGCGACAGAGGGAGACTCCATCTAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAATATTTTTCACTATAGAGAGGCATATGTCCCCTGAACTTGCCGGGATCCACCTTTCCTGCTGGTGCATTCTGTGAGTTAGAAGAAAACTTCCAAAGAGCCATTTTTTCCACCCTGTCTACTGTATAAAATTGCTTCTCAAACATGTGCTGCATTGCAGAGGATTACCATTGTTTTGCTAACCAGCGTCTGGTCTTTCTTATGTGGCGCTGCAATTACTAGTGTCAAACCCTGTTGGTAATACCCAGAGGATGGTGTCTGAAGTCTTTACTCAATATTCACATTGGCTGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTCGGAAGCAGAGGCAGGCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAATACAAAAATTAGCCGGGTATGGTGGCGGGTGCCTGTAATCTCAGCTACTAGGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGATTGTGCCACTGTACTCCAGCCTGGGGGAAAATTCACATTTGTAGAGAGTTTAAATTCTTTTTTGATACGGAGTCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCAGGGTCTTGACTCACTACAACCTCTGCCTCCCAGGCTCAAGGGATTCTCCTGCTTTAGCCTCCTGAGTAGTTGGGATTACAGGCACCCACCAAAACACCTGGGCAATTTTTGTATTTTTATTAGAGACAGGGTTTCACCATGTTGTCCAGGCTGATCTGAAACTCCTGACCTCAGGTGATCTGCCTGCCCTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCCGGCCGAGAGTTTAAATTCTTAAATCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCGTCTCAGTATTTCTATTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCAATTCCAGGTAAACTTTGGCCTTTTATGAATTCTCCTGATCAGGCCAAACCTCAACCAAGTCCCTTCTTGATCTTCTCCTTCACCTCCTTCCCTCATTCACCCAACAATTAGCCTCCAGTCCACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAAGCCTCAGCTAAAGTTTACAATCCTACCTTTTCTACTGCCTTGAAATGCCCTAAGGTTCAGGGGCTTCATGGTTGCTGCTTCATGGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCCGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTCTACAGCTCTGCTGTCCCATTAACAGCACCTTTGGGGCCCCAGGGTTCCAGATTGGAAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCTTTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTCTACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAGAGGATCTTTAGCCTGCGGCGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAAGGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGATCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAATAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGAGGAAAGGATGGAAACTACTACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCTTCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGTTTTTGTAGATTGAAGTCTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCCAGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGAAATCCTTCCACCTCAGCCCCCCAAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGTTAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAAGTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGTATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGGCCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCAAATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCATCTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGCTATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGAAGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGGCCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCCCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGAAAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACAGCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAATATCTGAGACCTAGCATGCTAGGAGACCTTTATCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAAATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGATGTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCA\t44\tCOV_CHANGE_INS\tPRECISE;SVTYPE=INS;SVLEN=7407;END=0;SUPPORT=3;COVERAGE=0,0,0,0,8;STRAND=+-;STDEV_LEN=16.000;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t./.:0:0:0",
+                "chr22\t10115\tSniffles2.INS.2S0\tA\tAATGTGAAATTGCAAATAATTCACCTGAGAAATGAAAATTAATCTTCTTTGCTAAATGCCATAGAGATATTTTAAGTTGCTAATGTTACTTAGATGTTCATTAACTTAGTGAGTTACATTAAGTAGAGAAGATGCCTTTTTTTTTTTCTGTACGAAGTCTTGCTCTGTAGCCCAGTGTAGTGGTATGATCTCGGCTCACCACAACCTCCGCCTCCTGTATTCAAGCGACTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGATTACAGGTGTGCACCATCGCACCTAGCTAATTTTTTGTATTTTTAGCAGAGACAGCATTTCACCATGTTGGCCAGGCTGTTCTTGAACCCCCGACCTCAGGTAATCCACCCTCCTTAGCCTCCCAAAGTGCCAGGATTACAGGCGTGAGCCACTGCACCCTGCTGAGAAGATGCCTTTTGACAATGAAGTGGATTTGTATATTTATCTTTGGCTTAAAAAAACATGCACCACCAATTACACTTTCCTCAAGTTTAAATTTTTAATAATTAGGAAAATAAAGCATTTTCTTGTCTTATAGTGTTAGCTAGATTGTTTTTGTGTATTTTGTCATGAATAAAAAGCATAGCTATATAGTTACTGCTTTTACATTAACTATAAATATCTTAAAATTTTACTACCTAAAATCAGGAAACTTGAACTGAAGCTACTAATCTTAGAGTTGGAAAAGTAAATACATAGAGGTTTCCTGTTGTACAAATGTCAAGTGGCACAGTGAAATTTACATTCATTTGAAAGTTTTCCTAACTGTAAAAAGTATCAAATTACTTGATACTTTGGAGTAGTTCATCATCTTTATCAGAGGCACAGGTCTTAACCATTGGCAAGCCTCTGTCAGAATATGCACATATTAAAGATCTGATTATTTTTGTGTTAATGTTAAAAAATTTTTCTGAAGCTTTTATCTTATTTTTTCCATCCTTACACCGTAAATTCACATTACCAAGTTGGGAAGCCAAAGAAACATTCTACTCTACTCATGTTTTTTCACCAGTTCATGAAAGTTGATGTTAGAAATGGGTGTGGGTGTGGGGGATGGGGGTGGTTGTACAGAAGCAGCAGGTGGTAGGGATAGGATTTCTGAAGCACTATCCTTGGCCTTTTTTGAGTAAACTCTTTATACCCTGAGCCACTTTCTTTTCAGAGGGCAATTGCTATTATTAGAGAGCCACCTTAAGCATTATTGTTGTAGAAAAATTAGGCACAACCAGTGATTGTCATTACAAGGACCAGCAAAAATGGCTAGGTTGCTACTCTGTATTTGTAACGCCCTTCCCCCAACAAAATTTCTCCTTTTCATATCTGTGAATTAGAAATAAGTGATAGAAAACTGTACTGCATTACAATATATACCATTTAATAAAACAAGTTTATAGTTGAGAGCACTATTCATGCTTTTTGAAAGAATGCAAATTTGTAATTTTTATGATAGCAATTCTTAATAATTTATTGTCCAAGAGATTTGATAAAATTTTTGATAGTTATTGGTCTCTGGGACTCAATAGGCACTGGAATGTTTTAATTCAGTTGAAAAGTTGGTTCAGGATTGCTACCCTCTCTTACCTGTTAGGAGGTTGTTGTTTAACCTGACCTGAAATTCCCATGAATAAGAACCTGTTTTTTTTTTTTTTTTTCTTTGACAGAGTCTTGCTCTGTCGCCCAGGCTGCAGTGCAGTGGTGCGATCTTGGCTCGCTGCAAGTTCCGCCTCCCAGGTTCAAGCGATTCTCCTGTCTCAGCCTCCCAAGTAGCTGGAGTAGCTGGGACTGCAGGCACGTACCACCATGCCTGACTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCGCAATCTCTTGACCTCATGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCACCTGGCCCAGGGAATTTCTAATATTTGAGAAGATGTTATTTTTAGTCTATTATACAAATTTATATATTGTTTACTAATATATAAATTTACATATTGGTTACTAATATGTAAACACCAATTTACATATTGGTTACTAATATGTAAACTTGATAAACATGGATTTCCATGGAAATTTAAAAGTATCACAACAATTTGTTTTCCCATTCTGAAACTTGTGATTTATTACATTTTCCTACTATTTCAGTTAATTCCATAATGCCAGATTTGTTGTAAATTTGCCGAGTGACAAGCCACACTGCTTCCTCTCATTCCTCTATTCCACAAAACTGCAAAGTTTCCCAGACCACAGTCAGGTTTCTCTGGGTTGTCCACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTAAGTCACTTTAAGTTTATGACGGAGGGGCTTCGTGAAACTTCATTGACCTTCCAAGGTGAAAATTGGTCAGTTTTCAGTTATAAAGGACATTAAGGATGGGTGTGGTGGCTGATACATGTAATCCCAGCACTTTCGGGAGACTCAGTCAGGAGGATCACTTAATCCTCATTTAAAAGGAGTTTGAGACCAGCCTGGGCAACAAAGTGAGGCCTTGTCTCTACAAAAAAATTAGCTGGGTGTGGTGGTAGGCACTTGTAGTCCCAACTACTCTGGAGACTGAGCTGAGAGAAGATTGTGTGAGGCTTGGAGGTTGAGGCTGCAGTGAACGGACATCACACCACTACACTCTAGTCAGGTGACAGAGCAAGACTCTAAATAAATAGGAACATTAGATGGTCTCTCTGCACTCTTGCCTGGTGGGGACGTGTTAGATACCCTCGTTAGGTTGTGATTTAGTTTTTAATCTGTGAGATGTTTGGGTCAAACAATTTTTAGCTGCCATGGAATAAACTTTCCAGTCAACGTGTGAGTTTGTGTTTGCCTTTACTTTTTTTTTTTTCTATATTGTTTTGGTCTATTTTTATCTTTTAATTTCAGAAAGCTGATTAATCTCTTCCTTTTCTCTTTAAAAATTTTCTTTATCATGTTTGTGCTACAGTGGTTATTTTGAGAACTTGTTGGCAGGATAAGTTGCAAAAGTTATGAAGTAGAATAGGGATGATTTCTGTTTTTGTTTTTTTTTTTTTCAGACAGAGTCTCACTCTCTTGCCTAGGCTGGAGTGCAGTGGCGTGATCCTGGCTCACTGCAGCCGCCGCCCTCCGGATTCAAGTGATTTGCCTGGCTCAGCCTCCCAAAAAGCTGGGATTACAGGTGCATGCCACCACACCCAGCTAATTTTTGTGTTTTTAGTAGAGATGGGTGTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCCGCACTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCATGCCTGGCTGAGATTATTTCTTTTTTTATTATAGCCATTGCTTGTAGATATATGCTGGTGGTTATCTGTAAAAATGTAATAGAAAGGCCGGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACAAGGTCAGGAGTGGGAGACCAGCCTGGCCAATATGGTAAAACCCCGTCTCTACCAAAAATACAAAAATTAGCTGGGCATAGTGGCGGGCACCTATAGTCCCAGTGACTCGGGAAGCTGAGGCAGGACAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGATCGTGCTATTATTGCACACCAGCCTGGGCGACAGAGTGAGACTCCGTCTCAAAAAAGAAAAAAGTAATAGACCAATCTTGAATTTATAATTGGAAGTGTTATTTCTTTATTTGCAGAATTTATTTATTTGTGACGCAGCTGTTGCTACCTCGCCTTTTCTTTTGTTGAGCTTAATCTCATGTCAAGTCATTCAACCAACTCAAAAGCGATGAAGACATTATTGAATCAACCTGAACTAAATCAGACCTAGGCTTCTTAAAATATACAGCTTAATGCTTCCAAATGATTTAGAAAACTAAAAAACCTAGCTACGCTGTAGGACACACAGTGGCCAATAAAAACAGGACCCCCAAACTGGCCAGTGGACCACTGCAACCACTATTTACTTCCTCCGTGTTTAGGAATGTTCAACGCTCCAAGCCCCATAGGCTGATTCAAGAAGATAAAGTGAGACTCAAGGAATTTCGAAGTGGAACAATACACCAAAGCCTTAAACCTGAAATGACTCTCCTTTTCTGGGGGTGAGGGAAGAAAAAGAAAAAGTTTCTAGGGCTCTCGGGGTGGCCTGGATGCCAGGGTCCCAGAAGTGGCCTTTTCTAGCTCCTGTAACTAAACCTGGCGGAAAACTCCCCGCCTGCTCACTCCACCCCCACCCGCCCAAGAATGCGTCTTCCCGTCTTCGGTGGCCCTACCCAGAATCCCAAAATGTGGGTTCCAACCCGGGCCCTGAATGTCTTCTCAAATCCCCGGGACCCAGGTTCCGGTGCGTGCCTTGCGTGCCGGGTCTTGCCCCTCGGGCGGTACCACCCAGGCAGCCCTAAATCCAGCCTCCCGGGCCCCCAGCAGCGCCCTCCGCCCCTCCACTATCCGGTCCGGCTCGAAGTCGGGGCCAAATCCAGAGACAAGAGGGCTGTGCCTGAAACTGAGCAGTTTCACCACTCGGCACTCCTGGCGGAAACTTCCCTTTAAAAAAAAAAAAAAAGAAAAGAAAGAAAAGCAACAGCACTTTTGGGCTAGCATTTCAATCCTTCCTGCCCTTTAGAGTTCCCAGTTCTGCTTCCAGCTGGCTTTGGGTGTTCCACTAGAATTGAGTTGTAAAGATATTCTTTAAGTGTTTATAGAACATTAAGACTTAAAAAAAATCTTTAAAATTAGAGGAGGGAAGCCACTGATCGCACACATCCAGGAAATGCAGCCCCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGACTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCGGTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGATCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAACTTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCCGCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTTCGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGATTCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGAGCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGGAAGCGCAGGAGCCGGCTGGGGGAGGGGGCGCCCTAGAGAAGCGGCTAGAAAGCTGAGACGGGGAACTGAGGTCATCCTGGGGGGGACAAGACAATGAGAGCCGGGCGCCTTGGGGGCGGCGCGGGAGCCTCCGCAGGACCAGGCGGGCGCCCCCTTTACCTGCGGCTCCGGCGCCTCGGCCGTTTCCTCGCGCGGCGGCGGCCGGGACTGAGCTGACACCACTCAGCCGGCGGGGTTTGAATGAGGAGGAGCGGGCGCGGAGGGGAGGGGGCGGGGAGGGAGGGAGGGAGGCGTCGCGGAGTTTCTCTCGGCCTTTTGTGCCATCCGCCGAGGCGCCTTGAGTATAAATCCAGATAGTGCAGTTTTTGTTGTGCTTGTGCTGATCAACTTTATGGTGTGATTAAATACGATTTTTTTTATTACGCTCTTGAAATTGTACTCTTGAGGTTGCAGAATGGCAATTAGATGGCAGTCGCTGATAGCCATGTAGAAGTTTTGATGAACATGCAAGTTAATTTTAATTTCTGATCAGTTACGGTTAGTGACTGTGGCCAAACATGTGCGTACTGATTCTACATGTGCTAATTCCGTGACGTTTATTCACCAGCTATGTGTCCCGTGCCTAATCCTGTGTCAGGCACCTTGTTCCAGGCATTGGGGGCAGCAGTGGACAAGGCAACAGAGTCTCCATCCTGAGGTGTTACTTTTAGAAAAAGATAGTTACAAGCAAATAAACAGGATGGTTTTAGATCTGGACAGAGGTTTTCAGAGGAAGTCATCCTTGAGCTGTCACAATGCTTTGGGGAGGGGTGTGCTGGGTAATCAGGGATGGCACATTTGGGGTGCCTAAGGATTGCTGTGGCCCTGGGAGCCTAGGACAGTTGGTCACAATTGACTTATTAGAGTCAGTCTCAGAAGCTTTCCTGGAAGTAGAATTGCTGCTGTTTTGCCAGGAGGGTTTCCTTCCCCATCTGACCACACAAGAAGACCCCTGCCCACAAATGCCTACCACTCCCAGGTCTCCCAGGCTGTTCACCCTCCCAGGCAAAGTGGAAGCTTCCTCTGTCCTAAGATCGTTTCCCACTGAACCTCCTTCATTTTCCTTCACTGCAGAGAAATAATCCTACAAGGTCTTGTGTGGAGAGTGATGGTACCTTCTTTAACCCAGATAATTGAGAATTGGAACCAAAACATCTGTGTATTAATAAATATTTTCAGTAACTAGGTTATGCTATTTCCCTGAGTGGGAAATAACACTCCATCATGTTTCTTTTTTTGGGGGGCAAGGGGGAGTCAAAGTTGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCGTGACTTGCACATATACATCCAGATGGCCTGAAGTAATTGAAGATCCACAGAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAATCTCCCCCACCCTTAAGAAGGTTCTTTGGAGTCTCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGACTGTAATTTTCCATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTCCCTTCACTTGACTCTCTTTTCAGACTCAGCCCACCTGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACGAAGCCTGTTTGGTGGTCTCTTCACACGGATGCGCATGAAATTTGGTGCCGTGACTTGGATCGGGGGACCTCCCTTAGGAGATCAATCCCCTGTCCTCCTGCTCTTTGCTCCGTGAGAAAGATCCACCTACGACCTCAGGTCCTCAGACCGACCAGCCCAAGAAACATCTCACCAATTTCAAATCTGGTAAGCGGCCTCTTTTTACTCTCTTCTCCATTCCTCCTCCTTCTCCCTTAGCTTCTCCAACCTCCCTCACTATCCCTCAACCTCTTTCTCCTTTCAATCTTGGCGCCACACTTCA\t7\tPASS\tPRECISE;SVTYPE=INS;SVLEN=7453;END=10115;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.300;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/1:10:7:3",
+                "chr22\t10126\tSniffles2.INS.1S0\tA\tACCGCTTTTCTGGGGCAGGGGCAAGTACCCCTCAACCCCTTCCCCTTCACACTTAGTGGCAAGTCCCGCTTTCCTGGGCAGGGGCAAGTACCCCTCAACGCCTTCTCCTTCACCCTTAGTGGCAAGTCCCGCTTTTCTAGGGGGGCAAGAACCCCCAAACCCCTTCCATCTGTGTCTCTACGCTCTCTTCTGTGGGTTTGCTTCCTTCACTATGGAACCTTCCACCCTCCATTCCTCCTTCTTCTCCCTTAGCCTGTGTGCTCAAAAAGTTAAAACCTCTTCAACTCACACCTGACCTAAAACCTAAATGCCTTATTTTCTTCTGCAACACCGCATATCTTGCTTGGCCCCAATACAAACTTGACAATGTCTCTAAATGGCCGGAAAATGGCACTTTGATTTCCCCACTGACAAACACCTAAATAATTTTTGTCGAAAAATGGGCAAATGGTCTGAGGTGCCTTACGTCCAGGCATTTTTCACACTTCGTTCCCTCCCTAGTCTCTGTTCCCAATGCGATTCCTCCCAGATCCTCCTCCTTTCCTCTCCTGTCCCCTCGGTCCCAACCCCAAGCGTCGCTGAGTCTTCCCAGTCTTCCTTTTCTACAGACCCATCTGACCTTTCCCCTCCTCCCCAAGCTGCTTGTCGCCAGACCGAGCTAAGTCCCAAGTACCTCCCTCAACTCTCCACTCCTCCACCCTATAATCCTTCTATCACCTCCCCTCCTCACACCTGGTCCGGCTTACAGTTTAGTTCCGCGACTAGCGCTTCCCCACCTGCCCAACAATTTCCTCTTAGAGAAAGTGGCTGGAGCTGAAGGCATAGTCAAGGGACATGTACTTTTTTCTCTATCAGACCTCTCTCAGATCAGTCAATGTTTAGGCTCTTTCTCATCAGACCCCACTAAATATATACAGGAATTCCAATATCTAACTCTGTCCTACAACTTAACCTGGAGTGACTTAAATGTCATCCTGACTTCTACTCTCTCCCCAATATGAACGGGAAAGTTTTTTCTCTAGCCCAATCTCGTGCTGATAACCGCCGGCTTCATGAGCCAGACCTCCAGGAAGGCATTAGAGCAGTTCCCCGAGAGGATCCCCAATGGAACTATCAGGCAGATTCCCCAGGTACAGCTAGGCGAGATTACATGGTTTCCTGCCTAGTTGAAGGGCTTAAAAAAGCAGCTTACAAAGCTGTTAATTATGACAAGCTTAAAGAAACTACCCGAGGTAAAGACGAAAACCCAGCCCAGGTCATGGCCCACTTAGCAGCAACCATTAGATGCTATACTGCCCTAGACCCAGAGGGGCCAGAAGGCCGCCTTATTCTTAATATGCATTTTTATCACCCAATCCACTCCTGACATTAGGAAAAAACTTCAAAAATTAGAATCTGGCCTTCAAACCCAGCAGGAATTAATCAACCTTGCCTTCAAGGTGTACAATAATAGAGAGGAAGCAGCCAGACGGCAACGCATTTCGAGTTACAATTACTTGCCTCTGCTGTGAGACAAAACCCAGCCACACCTCCTGCATACAGGAACTTCAAAATGCCTAAGCCGCAGCAATCAGACACTCCTACAAGACTTCATCAGGATCTTGCTTCAAGTGCCAGAAATCTGGCCACTGGGCCAAGGAATGCCCACAGCCCAGGATTCCTCCCAAGCCATGTCCCATCTGTGCAGGCACCCACTGGAAATCAGACTGCCCAGCTCGCCCGACAGCCACTCCTGGAGCCCCTAAAGCTCTAGCCCAAGGCTCTCTGACTCCTTCCCAGATCTATTCGGCTTAGCGACTGAAGATTGACGCTGCCCGATCGCCTCGGAAGTCCCCTGGACCATCACAGAAGCCGAGCTTCGGGTAACTCTCACAGTGGAGGGTAAGTCCATCCCCTGTTTAATCGATACGGGGGCTACCCACTCCACGTTGCCTTCTTTTCAAGGGCCTGTTTCCCTTGCCCCCATAACTGTTGTGGGTATTGACGGCCAAGCTTCAAAACCCCTGAAAACTCCCCCACTCTGGTGCCAACTTGGACAACACTCTTTTATGCACTCTTTTTTAGTTATCCCCACCTGCCCACTTCCCTTATTAGGCCGAAATATTTTAACCAAATTATCTGCTTCCCTGACTATTCCTGGAGTACAGCTACATCTCATTGCTGCCCTTCTTCCCAATCCAAAGCCTCCTTTGTGTCCTCTAACATCCCCACAATATCACCCCTTACCACAAGACCTCCCTTCAGCTTAATCTCTCCCACTCTAGGTTCCCACGCCGCCCCTAATCCCACTTGAAGCAGCCCTGAGAAACATCGTCCATTCTCTCTCCATACCACCCCCCAAAAATTTTCGCCGCTCCAACACTTCAACACTATTTTGTTTTATTTGTCTTATTAATATCAGAAGGCAGGAATGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCCTGTGACTTGCACGTATACATCCAGATGGCCTGAAGTAACTGAAGATCCACAAAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAGACTCCCTCCCCCCACCCTTAAGAAGGTTCTTTGTAATTCTCCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGATTGTAATTTTTTATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTTCCTTCACTGAACTCTCTTTTCGGACTCAGCCCACCGGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGTATGAAAAAAGTCTCGCCCTGTTGCCCAGGCTGGAATGCAGTGGCACGATCTTGGCTCACTGCTACCTCCACTTCCTGGGTTCAAGTGATTCCCAAGTAGCTGGGATTACAGGTGTGTATTACCATGCCCAGCTAATTTTTGTATTTTTAGCAGATAAGGGGTTTCACCATGTTGGCCAGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACTTCGGCTACCCAAAGCATTGGGAGTACAGGGGTGAGCCACTATGCCCAGCCTCACATCATATTTCTAATCCCGAGACTGTAGAGCTGGTGTCTCTTTTTGGAAAGGATGTCAGTAGAGAAAATGGAGTTCCCCAAAATTACAGTTTCACATATTAGTAAAGTTTCTAAAATACAGTAATAATGTTGAGAGCTGACATAGGGACTAACTTAGTTTTTTTTTTTTTTTAGATTGTCACCTAACTTTGATTTTGCTAAATAAGGACATTAAAAGAAAACCAAAAAAGTCCACTATTGGCTATTGCCACTATTTGATTTTTTAAAAAATAAGCGTATTTTAGCATCTAAAAGTAGGAAGGACCTCAAATAAATGAGTCTTTGTTCTTGGCCAGGGAAACAGCGTTGTCAGCATTTGATAACTGTTTTTCTAGGGTATGTGCTGTTATTCAGTTAAAACCTTGCCTGGGGATGTTAGCATTGGTAAATACTTGTTGAATAAGCAAATGAAACTTAAGCTTCTATGTATAGAAACCTAAGTCACTTCACATTCTGATTAGCAGAGTAATTGAATATTCTTTTCAGTGTGTAGATCTATACCCAGAACCACAGAATATCGGAACTGTAAAAACCAACTGCATTAAATAGATGTGGTATGTGGCAGTGTACCAAGGTTGTGACTAGAACTCCGGTCTTGGAGTGTTCTATTATATCACACCAAGCTGGTCACCAGCCCATGTGTTGATCCTCCATTGTGATAGCAACAAAGAAAAGACTTCAGGACATTCTTTCCTTTACCCTAATCCTTCATCTTCAGTCTTATTTAGAAAAGCTTAATGTTAAAGATCTAGTTTATTCAAAACTAAAGATAAGGAGTATGAGAATTTCTATTTCGGAGTGTAAAGGAGGAGATGTTTCCTTGGCTTCTCTGAGCCTACAGGCCTTCCTTGCTCTTTAAGGAAGTAGAGAGAGAGAGGAAAGTAAAGTATGCTTTTGTTTTTTAAGGTTACTTTGCTGGGAGTAGTTTGCATGCCATTTGGTTTTCTTGGGTGGAATTAACTGACTTAAGTTTTAAGTAGTTGGGACTATTTAGAAACAATGCCTATCCAATGTTTGCCATAAAGGCAGAGGGTATTGGCTTTAGAAGTTAATTCTTCTCCAGGAGTGAAAATGAGCTGCTAAACCAGAAGCAGCAGAGCTAAAGAAAGTAATTTTCCACCTGGCCAGTGCATGATGTGAAAGGTAGACTAAAAGAATGAGAGGACCCATTTTCTGATGAAAGACTAAGCCATGTTGAAACAGCCCTGTTGAGGATTTTATTTTAAATCTATACATTCACAAAGGAGCTTTGTGTATGTCTTTCCCTATTTGTTGTTTGGACTAAGGGAGCCCCACCCAGTGCTTGTTCAGTAAGTTGTTGAAAGAAATCTGGATTTGAACAGTGGATTGAGGTTTCGAATATCCAGTGAACCAAAATATATCAGGGTTCCCCTGGCCAAGATGAGTGACCATTCTGAGGTGTTACGTATTTCTTGAATGGGGATTTTAGGAAAAGTTTCTGTATTTCTGTGCTCATTTTGTTGACCTCTGTATGTGCAAAATCTCTAAGGGGGTGTTTGGGCACTTAGATTTCTTGGATGCAGATTTGTTTGTATATGAAACAAATTTTAAATTGTTTCGTATACACTGGATTTAAAATAGTTTAGTTTACTAAAGTGTTTTAATGTTTTCATCTTAATTTTCAGTTCTTATAGTCTTTAGATTTAGGGAGGCTGTTGATGGCATCCACATATGCATTTTAATGTCATTTAAAATGTATTCTGCTGAATTTAACAATTTCTGACCTAAAACTTGACATTTTAATATTTAAGTCGGTAAAGCGCTGATTTAAACTGGATTTTAACTGGATGAAATTCTGATTTAATGAGTGTACTGACTGGATAAAATGCCAATGATTTAATTAACAAGCACGTTTACAGCATGCCCTATATATTAGTTAAAAGTGAAGCAATTGAATTAGGTACCATTTCAAAATGGTTGCTGTACCCACTCACCCTCTCTATCCTCCAATTAGGGTATATTTTGAAATGATTGCTTTTCCCTTTTCCTTGTGTAAAGAGCCTGAGGAAATTTTCTTCGGCCTTCATCATGAGAACCTGGTGGGGTTTCTGGAAGTAAAATTCATGAAAGTATAAGGGGCCCCCAAGACGGGACTCCAACAAGTTTTTAACTCTCAAGCTAGTCCACACTCAGCCACCAGTAAATTTATTGATTACCATTGAAGTGTTCCTACCAATTAC\t9\tPASS\tPRECISE;SVTYPE=INS;SVLEN=5362;END=10126;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.200;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:2:8:2",
+                "chr22\t13000\tSniffles2.INS.3S0\tT\tTGATAATCAAGAGAACGTCTCAGCACCGCGCCTGAGCGCTTAGTAGGTAGTGATCAAGAGAGAAGACCTC\t36\tGT\tIMPRECISE;SVTYPE=INS;SVLEN=69;END=13000;SUPPORT=2;COVERAGE=11,13,13,16,51;STRAND=+-;AF=0.154;STDEV_LEN=6.364;STDEV_POS=37.477;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:10:11:2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-30T13:26:44.362217872"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sniffles/tests/nextflow.config b/modules/nf-core/sniffles/tests/nextflow.config
new file mode 100644
index 00000000..06e38362
--- /dev/null
+++ b/modules/nf-core/sniffles/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'SNIFFLES' {
+        ext.args = '--minsupport 1 --no-qc --mapq 0'
+        }
+}
diff --git a/modules/nf-core/sniffles/tests/tags.yml b/modules/nf-core/sniffles/tests/tags.yml
new file mode 100644
index 00000000..7010d53c
--- /dev/null
+++ b/modules/nf-core/sniffles/tests/tags.yml
@@ -0,0 +1,2 @@
+sniffles:
+  - "modules/nf-core/sniffles/**"
diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml
index fe32ebda..757967b2 100644
--- a/modules/nf-core/somalier/extract/environment.yml
+++ b/modules/nf-core/somalier/extract/environment.yml
@@ -1,7 +1,5 @@
-name: somalier_extract
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::somalier=0.2.18
diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml
index aabaf5d6..25621667 100644
--- a/modules/nf-core/somalier/extract/meta.yml
+++ b/modules/nf-core/somalier/extract/meta.yml
@@ -1,5 +1,6 @@
 name: "somalier_extract"
-description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
+description: Somalier can extract informative sites, evaluate relatedness, and perform
+  quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
 keywords:
   - relatedness
   - QC
@@ -14,65 +15,69 @@ keywords:
   - family
 tools:
   - "somalier":
-      description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
+      description: "Somalier can extract informative sites, evaluate relatedness, and
+        perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
       homepage: "https://github.com/brentp/somalier"
       documentation: "https://github.com/brentp/somalier/blob/master/README.md"
       tool_dev_url: "https://github.com/brentp/somalier"
       doi: "10.1186/s13073-020-00761-2"
       licence: ["MIT"]
+      identifier: biotools:somalier
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file
-  - input_index:
-      type: file
-      description: index file of the input data, e.g., bam.bai, cram.crai
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'hg38' ]
-  - fasta:
-      type: file
-      description: The reference fasta file
-      pattern: "*.{fasta,fna,fas,fa}"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'hg38' ]
-  - fai:
-      type: file
-      description: FASTA index file
-      pattern: "*.fai"
-  - meta4:
-      type: map
-      description: |
-        Groovy Map containing sites information
-        e.g. [ id:'hg38' ]
-  - sites:
-      type: file
-      description: sites file in VCF format which can be taken from https://github.com/brentp/somalier
-      pattern: "*.vcf.gz"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file
+    - input_index:
+        type: file
+        description: index file of the input data, e.g., bam.bai, cram.crai
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'hg38' ]
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.{fasta,fna,fas,fa}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'hg38' ]
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sites information
+          e.g. [ id:'hg38' ]
+    - sites:
+        type: file
+        description: sites file in VCF format which can be taken from https://github.com/brentp/somalier
+        pattern: "*.vcf.gz"
 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"
   - extract:
-      type: file
-      description: binary output file based on extracted sites
-      pattern: "*.{somalier}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.somalier":
+          type: file
+          description: binary output file based on extracted sites
+          pattern: "*.{somalier}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ashotmarg"
   - "@nvnieuwk"
diff --git a/modules/nf-core/somalier/extract/somalier-extract.diff b/modules/nf-core/somalier/extract/somalier-extract.diff
index 59f472ab..b1118b5e 100644
--- a/modules/nf-core/somalier/extract/somalier-extract.diff
+++ b/modules/nf-core/somalier/extract/somalier-extract.diff
@@ -1,4 +1,6 @@
 Changes in module 'nf-core/somalier/extract'
+'modules/nf-core/somalier/extract/meta.yml' is unchanged
+Changes in 'somalier/extract/main.nf':
 --- modules/nf-core/somalier/extract/main.nf
 +++ modules/nf-core/somalier/extract/main.nf
 @@ -5,8 +5,8 @@
@@ -13,13 +15,17 @@ Changes in module 'nf-core/somalier/extract'
      input:
      tuple val(meta), path(input), path(input_index)
 
+Changes in 'somalier/extract/environment.yml':
 --- modules/nf-core/somalier/extract/environment.yml
 +++ modules/nf-core/somalier/extract/environment.yml
-@@ -4,4 +4,4 @@
+@@ -2,4 +2,4 @@
+   - conda-forge
    - bioconda
-   - defaults
  dependencies:
 -  - bioconda::somalier=0.2.19
 +  - bioconda::somalier=0.2.18
 
+'modules/nf-core/somalier/extract/tests/tags.yml' is unchanged
+'modules/nf-core/somalier/extract/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/somalier/extract/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml
index 3a730471..757967b2 100644
--- a/modules/nf-core/somalier/relate/environment.yml
+++ b/modules/nf-core/somalier/relate/environment.yml
@@ -1,7 +1,5 @@
-name: somalier_relate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::somalier=0.2.18
diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml
index 42638f4f..0da72821 100644
--- a/modules/nf-core/somalier/relate/meta.yml
+++ b/modules/nf-core/somalier/relate/meta.yml
@@ -1,5 +1,6 @@
 name: "somalier_relate"
-description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
+description: Somalier can extract informative sites, evaluate relatedness, and perform
+  quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
 keywords:
   - relatedness
   - QC
@@ -14,47 +15,67 @@ keywords:
   - family
 tools:
   - "somalier":
-      description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
+      description: "Somalier can extract informative sites, evaluate relatedness, and
+        perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
       homepage: "https://github.com/brentp/somalier"
       documentation: "https://github.com/brentp/somalier/blob/master/README.md"
       tool_dev_url: "https://github.com/brentp/somalier"
       doi: "10.1186/s13073-020-00761-2"
       licence: ["MIT"]
+      identifier: biotools:somalier
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - extract:
-      type: file
-      description: extract file(s) from Somalier extract
-      pattern: "*.somalier"
-  - ped:
-      type: file
-      description: optional path to a ped or fam file indicating the expected relationships among samples
-      pattern: "*.{ped,fam}"
-  - sample_groups:
-      type: file
-      description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
-      pattern: "*.{txt,csv}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - extract:
+        type: file
+        description: extract file(s) from Somalier extract
+        pattern: "*.somalier"
+    - ped:
+        type: file
+        description: optional path to a ped or fam file indicating the expected relationships
+          among samples
+        pattern: "*.{ped,fam}"
+  - - sample_groups:
+        type: file
+        description: optional path to expected groups of samples such as tumor normal
+          pairs specified as comma-separated groups per line
+        pattern: "*.{txt,csv}"
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - html:
-      type: file
-      description: html file
-      pattern: "*.html"
+      - meta:
+          type: file
+          description: html file
+          pattern: "*.html"
+      - "*.html":
+          type: file
+          description: html file
+          pattern: "*.html"
   - pairs_tsv:
-      type: file
-      description: tsv file with output stats for pairs of samples
-      pattern: "*.pairs.tsv"
+      - meta:
+          type: file
+          description: tsv file with output stats for pairs of samples
+          pattern: "*.pairs.tsv"
+      - "*.pairs.tsv":
+          type: file
+          description: tsv file with output stats for pairs of samples
+          pattern: "*.pairs.tsv"
   - samples_tsv:
-      type: file
-      description: tsv file with sample-level information
-      pattern: "*.samples.tsv"
+      - meta:
+          type: file
+          description: tsv file with sample-level information
+          pattern: "*.samples.tsv"
+      - "*.samples.tsv":
+          type: file
+          description: tsv file with sample-level information
+          pattern: "*.samples.tsv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ashotmarg"
   - "@nvnieuwk"
diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff
index f583d612..7dd8b76c 100644
--- a/modules/nf-core/somalier/relate/somalier-relate.diff
+++ b/modules/nf-core/somalier/relate/somalier-relate.diff
@@ -1,4 +1,6 @@
 Changes in module 'nf-core/somalier/relate'
+'modules/nf-core/somalier/relate/meta.yml' is unchanged
+Changes in 'somalier/relate/main.nf':
 --- modules/nf-core/somalier/relate/main.nf
 +++ modules/nf-core/somalier/relate/main.nf
 @@ -5,8 +5,8 @@
@@ -13,13 +15,17 @@ Changes in module 'nf-core/somalier/relate'
      input:
      tuple val(meta), path(extract), path(ped)
 
+Changes in 'somalier/relate/environment.yml':
 --- modules/nf-core/somalier/relate/environment.yml
 +++ modules/nf-core/somalier/relate/environment.yml
-@@ -4,4 +4,4 @@
+@@ -2,4 +2,4 @@
+   - conda-forge
    - bioconda
-   - defaults
  dependencies:
 -  - bioconda::somalier=0.2.19
 +  - bioconda::somalier=0.2.18
 
+'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged
+'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/splitubam/environment.yml b/modules/nf-core/splitubam/environment.yml
index ef128202..382f9112 100644
--- a/modules/nf-core/splitubam/environment.yml
+++ b/modules/nf-core/splitubam/environment.yml
@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "splitubam"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::splitubam=0.1.1"
diff --git a/modules/nf-core/splitubam/meta.yml b/modules/nf-core/splitubam/meta.yml
index 3d11eaae..64691357 100644
--- a/modules/nf-core/splitubam/meta.yml
+++ b/modules/nf-core/splitubam/meta.yml
@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "splitubam"
 description: split one ubam into multiple, per line, fast
@@ -13,33 +12,34 @@ tools:
       documentation: "https://github.com/fellen31/splitubam"
       tool_dev_url: "https://github.com/fellen31/splitubam"
       licence: ["MIT"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:true ]`
-  - bam:
-      type: file
-      description: (u)BAM file
-      pattern: "*.{bam}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:true ]`
+    - bam:
+        type: file
+        description: (u)BAM file
+        pattern: "*.{bam}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - bam:
-      type: file
-      description: Split (u)BAM file
-      pattern: "*.{bam}"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.bam":
+          type: file
+          description: Split (u)BAM file
+          pattern: "*.{bam}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@fellen31"
 maintainers:
diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml
index 530ce375..c476e2b3 100644
--- a/modules/nf-core/stranger/environment.yml
+++ b/modules/nf-core/stranger/environment.yml
@@ -1,7 +1,5 @@
-name: stranger
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::stranger=0.9.1
+  - bioconda::stranger=0.9.2
diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf
index 923483f4..bc31e703 100644
--- a/modules/nf-core/stranger/main.nf
+++ b/modules/nf-core/stranger/main.nf
@@ -4,8 +4,8 @@ process STRANGER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stranger:0.9.1--pyh7e72e81_0':
-        'biocontainers/stranger:0.9.1--pyh7e72e81_0' }"
+        'https://depot.galaxyproject.org/singularity/stranger:0.9.2--pyh7e72e81_0':
+        'biocontainers/stranger:0.9.2--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml
index 5e0bc0bb..a5486dbd 100644
--- a/modules/nf-core/stranger/meta.yml
+++ b/modules/nf-core/stranger/meta.yml
@@ -1,5 +1,6 @@
 name: stranger
-description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
+description: Annotates output files from ExpansionHunter with the pathologic implications
+  of the repeat sizes.
 keywords:
   - STR
   - repeat_expansions
@@ -13,39 +14,42 @@ tools:
       tool_dev_url: https://github.com/moonso/stranger
       doi: "10.5281/zenodo.4548873"
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: VCF with repeat expansions
-      pattern: "*.{vcf.gz,vcf}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test' ]
-  - variant_catalog:
-      type: file
-      description: json file with repeat expansion sites to genotype
-      pattern: "*.{json}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF with repeat expansions
+        pattern: "*.{vcf.gz,vcf}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - variant_catalog:
+        type: file
+        description: json file with repeat expansion sites to genotype
+        pattern: "*.{json}"
 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"
   - vcf:
-      type: file
-      description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
-      pattern: "*.{vcf.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gz":
+          type: file
+          description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
+          pattern: "*.{vcf.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@ljmesi"
 maintainers:
diff --git a/modules/nf-core/stranger/tests/main.nf.test b/modules/nf-core/stranger/tests/main.nf.test
index 13c61f43..3c12a2c5 100644
--- a/modules/nf-core/stranger/tests/main.nf.test
+++ b/modules/nf-core/stranger/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             script "../../expansionhunter/main.nf"
             process {
                 """
-                 input[0] = [
+                input[0] = [
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
diff --git a/modules/nf-core/stranger/tests/main.nf.test.snap b/modules/nf-core/stranger/tests/main.nf.test.snap
index 3faa4e58..b0ce7380 100644
--- a/modules/nf-core/stranger/tests/main.nf.test.snap
+++ b/modules/nf-core/stranger/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c"
+                    "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb"
                 ],
                 "vcf": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c"
+                    "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-03T08:09:27.725425094"
+        "timestamp": "2024-11-04T10:27:41.164430492"
     },
     "homo_sapiens - vcf, repeat_catalogue": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c"
+                    "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb"
                 ],
                 "vcf": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c"
+                    "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-03T08:09:14.472394433"
+        "timestamp": "2024-11-04T10:27:31.05008915"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/stranger/tests/nextflow.config b/modules/nf-core/stranger/tests/nextflow.config
index 98459330..0ddc8bbd 100644
--- a/modules/nf-core/stranger/tests/nextflow.config
+++ b/modules/nf-core/stranger/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
-     withName: 'STRANGER' {
-         ext.prefix = "stranger"
-     }
- }
+    withName: 'STRANGER' {
+        ext.prefix = "stranger"
+    }
+}
diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml
new file mode 100644
index 00000000..ab87ec70
--- /dev/null
+++ b/modules/nf-core/svdb/merge/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bcftools=1.21
+  - svdb=2.8.2
diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf
new file mode 100644
index 00000000..24c5effd
--- /dev/null
+++ b/modules/nf-core/svdb/merge/main.nf
@@ -0,0 +1,105 @@
+process SVDB_MERGE {
+    tag "$meta.id"
+    label 'process_single'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd:b3615e06ef17566f2988a215ce9e10808c1d08bf-0':
+        'biocontainers/mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd:b3615e06ef17566f2988a215ce9e10808c1d08bf-0' }"
+
+    input:
+    tuple val(meta), path(vcfs)
+    val(input_priority)
+    val(sort_inputs)
+
+    output:
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def args2   = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // Ensure priority list matches the number of VCFs if priority is provided
+    if (input_priority && vcfs.collect().size() != input_priority.collect().size()) {
+        error "If priority is used, one tag per VCF is needed"
+    }
+
+    def input = ""
+    def prio = ""
+    if (input_priority) {
+        if (vcfs.collect().size() > 1 && sort_inputs) {
+            // make vcf-prioprity pairs and sort on VCF name, so priority is also sorted the same
+            def pairs = vcfs.indices.collect { [vcfs[it], input_priority[it]] }
+            pairs = pairs.sort { a, b -> a[0].name <=> b[0].name }
+            vcfs = pairs.collect { it[0] }
+            priority = pairs.collect { it[1] }
+        } else {
+            priority = input_priority
+        }
+
+        // Build inputs
+        prio = "--priority ${input_priority.join(',')}"
+        input = ""
+        for (int index = 0; index < vcfs.collect().size(); index++) {
+            input += "${vcfs[index]}:${priority[index]} "
+        }
+
+    } else {
+        // if there's no priority input just sort the vcfs by name if possible
+        input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { it.name } : vcfs
+    }
+
+    def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" :
+                    args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" :
+                    args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" :
+                    args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
+                    "vcf.gz"
+    """
+    svdb \\
+        --merge \\
+        $args \\
+        $prio \\
+        --vcf $input |\\
+        bcftools view \\
+            $args2 \\
+            --threads ${task.cpus} \\
+            --output ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args2   = task.ext.args2 ?: ''
+    def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" :
+                    args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" :
+                    args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" :
+                    args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
+                    "vcf.gz"
+    def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" :
+                args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" :
+                args2.contains("--write-index") || args2.contains("-W") ? "csi" :
+                ""
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+    """
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml
new file mode 100644
index 00000000..c34a9cb1
--- /dev/null
+++ b/modules/nf-core/svdb/merge/meta.yml
@@ -0,0 +1,77 @@
+name: svdb_merge
+description: The merge module merges structural variants within one or more vcf files.
+keywords:
+  - structural variants
+  - vcf
+  - merge
+tools:
+  - svdb:
+      description: structural variant database software
+      homepage: https://github.com/J35P312/SVDB
+      documentation: https://github.com/J35P312/SVDB/blob/master/README.md
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - vcfs:
+        type: list
+        description: |
+          One or more VCF files. The order and number of files should correspond to
+          the order and number of tags in the `priority` input channel.
+        pattern: "*.{vcf,vcf.gz}"
+  - - input_priority:
+        type: list
+        description: |
+          Prioritize the input VCF files according to this list,
+          e.g ['tiddit','cnvnator']. The order and number of tags should correspond to
+          the order and number of VCFs in the `vcfs` input channel.
+  - - sort_inputs:
+        type: boolean
+        description: |
+          Should the input files be sorted by name. The priority tag will be sorted
+          together with it's corresponding VCF file.
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: VCF output file
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@ramprasadn"
+maintainers:
+  - "@ramprasadn"
+  - "@fellen31"
diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test
new file mode 100644
index 00000000..6a79d7a0
--- /dev/null
+++ b/modules/nf-core/svdb/merge/tests/main.nf.test
@@ -0,0 +1,360 @@
+nextflow_process {
+
+    name "Test Process SVDB_MERGE"
+    script "modules/nf-core/svdb/merge/main.nf"
+    config "./nextflow.config"
+    process "SVDB_MERGE"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svdb"
+    tag "svdb/merge"
+
+    test("1 sample, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--vcf test.vcf") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample, [], true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--vcf test.vcf") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample, ['tiddit'], []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ])
+                input[1] = ['tiddit']
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--priority tiddit --vcf test.vcf:tiddit") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample, ['tiddit'], true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ])
+                input[1] = ['tiddit']
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--priority tiddit --vcf test.vcf:tiddit") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("2 samples, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--vcf test2.vcf test.vcf") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("2 samples, [], true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = []
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--vcf test.vcf test2.vcf") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("2 samples, ['tiddit', 'cnvnator'], []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = ['tiddit', 'cnvnator']
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--priority tiddit,cnvnator --vcf test2.vcf:tiddit test.vcf:cnvnator") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("2 samples, ['tiddit', 'cnvnator'], true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = ['tiddit', 'cnvnator']
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip[3].contains("--priority tiddit,cnvnator --vcf test.vcf:cnvnator test2.vcf:tiddit") }, // SVDB command line
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("2 samples, [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("2 samples, [], true - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = []
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("2 samples, ['tiddit', 'cnvnator'], [] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = ['tiddit', 'cnvnator']
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("2 samples, ['tiddit', 'cnvnator'], true - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                    ]
+                ])
+                input[1] = ['tiddit', 'cnvnator']
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test.snap b/modules/nf-core/svdb/merge/tests/main.nf.test.snap
new file mode 100644
index 00000000..e86662e5
--- /dev/null
+++ b/modules/nf-core/svdb/merge/tests/main.nf.test.snap
@@ -0,0 +1,294 @@
+{
+    "1 sample, [], []": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]",
+            "60fb4cab2aa891bebef8ffdbd0e41bc3",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:00:25.9277471"
+    },
+    "2 samples, ['tiddit', 'cnvnator'], true - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:05:49.325618245"
+    },
+    "2 samples, ['tiddit', 'cnvnator'], []": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]",
+            "254e56e4fc8356d68424828438da66e3",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:02:27.964808463"
+    },
+    "2 samples, [], []": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]",
+            "7ad648266e57d405b5b01aaea4613d1c",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:02:11.013532413"
+    },
+    "2 samples, ['tiddit', 'cnvnator'], true": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]",
+            "254e56e4fc8356d68424828438da66e3",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:02:35.956320871"
+    },
+    "1 sample, ['tiddit'], []": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]",
+            "9dd588cd870672b78192f48ad440b5d",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:00:42.064583463"
+    },
+    "1 sample, [], true": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]",
+            "60fb4cab2aa891bebef8ffdbd0e41bc3",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:00:33.88572601"
+    },
+    "1 sample, ['tiddit'], true": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]",
+            "9dd588cd870672b78192f48ad440b5d",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:00:50.18149857"
+    },
+    "2 samples, [], true": {
+        "content": [
+            "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]",
+            "de0a3b56cdee89e4c9cd4fbb4ad3391d",
+            [
+                "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:02:19.556799178"
+    },
+    "2 samples, ['tiddit', 'cnvnator'], [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:05:40.427970257"
+    },
+    "2 samples, [], [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:05:24.34471465"
+    },
+    "2 samples, [], true - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T09:05:32.529261733"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svdb/merge/tests/nextflow.config b/modules/nf-core/svdb/merge/tests/nextflow.config
new file mode 100644
index 00000000..c267037c
--- /dev/null
+++ b/modules/nf-core/svdb/merge/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: 'SVDB_MERGE' {
+        ext.prefix = "merged"
+        ext.args2 = '--output-type z --no-version'
+    }
+}
diff --git a/modules/nf-core/svdb/merge/tests/tags.yml b/modules/nf-core/svdb/merge/tests/tags.yml
new file mode 100644
index 00000000..8501d907
--- /dev/null
+++ b/modules/nf-core/svdb/merge/tests/tags.yml
@@ -0,0 +1,2 @@
+svdb/merge:
+  - modules/nf-core/svdb/merge/**
diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml
new file mode 100644
index 00000000..2af55220
--- /dev/null
+++ b/modules/nf-core/svdb/query/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::svdb=2.8.2
diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf
new file mode 100644
index 00000000..4ceb477a
--- /dev/null
+++ b/modules/nf-core/svdb/query/main.nf
@@ -0,0 +1,77 @@
+process SVDB_QUERY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svdb:2.8.2--py39h5371cbf_0':
+        'biocontainers/svdb:2.8.2--py39h5371cbf_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+    val(in_occs)
+    val(in_frqs)
+    val(out_occs)
+    val(out_frqs)
+    path(vcf_dbs)
+    path(bedpe_dbs)
+
+    output:
+    tuple val(meta), path("*_query.vcf")    , emit: vcf
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args             = task.ext.args ?: ''
+    def prefix           = task.ext.prefix ?: "${meta.id}"
+    def in_occ           = ""
+    def in_frq           = ""
+    def out_occ          = ""
+    def out_frq          = ""
+    def dbs_argument     = vcf_dbs  ? "--db ${vcf_dbs.join(',')}" : ''
+    def bedpeds_argument = bedpe_dbs ? "--bedpedb ${bedpe_dbs.join(',')}" : ''
+    if (in_occs) {
+        in_occ  = "--in_occ ${in_occs.join(',')}"
+    }
+    if (in_frqs) {
+        in_frq  = "--in_frq ${in_frqs.join(',')}"
+    }
+    if (out_occs) {
+        out_occ = "--out_occ ${out_occs.join(',')}"
+    }
+    if (out_frqs) {
+        out_frq = "--out_frq ${out_frqs.join(',')}"
+    }
+    if ( vcf_dbs && bedpe_dbs ) error "bedpedb input is not compatible with db inputs"
+    """
+    svdb \\
+        --query \\
+        $in_occ \\
+        $in_frq \\
+        $out_occ \\
+        $out_frq \\
+        $args \\
+        $dbs_argument \\
+        $bedpeds_argument \\
+        --query_vcf $vcf \\
+        --prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_query.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml
new file mode 100644
index 00000000..f8cd33c8
--- /dev/null
+++ b/modules/nf-core/svdb/query/meta.yml
@@ -0,0 +1,63 @@
+name: svdb_query
+description: Query a structural variant database, using a vcf file as query
+keywords:
+  - structural variants
+  - query
+  - svdb
+tools:
+  - svdb:
+      description: structural variant database software
+      homepage: https://github.com/J35P312/SVDB
+      documentation: https://github.com/J35P312/SVDB/blob/master/README.md
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: query vcf file
+        pattern: "*.{vcf,vcf.gz}"
+  - - in_occs:
+        type: list
+        description: A list of allele count tags
+  - - in_frqs:
+        type: list
+        description: A list of allele frequency tags
+  - - out_occs:
+        type: list
+        description: A list of allele count tags
+  - - out_frqs:
+        type: list
+        description: A list of allele frequency tags
+  - - vcf_dbs:
+        type: file
+        description: path to a database vcf, or a comma separated list of vcfs
+        pattern: "*.{vcf,vcf.gz}"
+  - - bedpe_dbs:
+        type: file
+        description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency,
+          or a comma separated list of files
+        pattern: "*.{bedpe}"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*_query.vcf":
+          type: file
+          description: Annotated output VCF file
+          pattern: "*_query.vcf"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@ramprasadn"
diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test
new file mode 100644
index 00000000..72e82915
--- /dev/null
+++ b/modules/nf-core/svdb/query/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process SVDB_QUERY"
+    script "modules/nf-core/svdb/query/main.nf"
+    process "SVDB_QUERY"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svdb"
+    tag "svdb/query"
+
+    test("svdb query") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test' ], // meta map
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ]
+                        ])
+                input[1] = ['AC']
+                input[2] = ['AF']
+                input[3] = ['gnomad_svAC']
+                input[4] = ['gnomad_svAF']
+                input[5] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz', checkIfExists: true)])
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(file(process.out.vcf[0][1]).name, file(process.out.versions[0]).name).match()}
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap
new file mode 100644
index 00000000..65f2fcfa
--- /dev/null
+++ b/modules/nf-core/svdb/query/tests/main.nf.test.snap
@@ -0,0 +1,13 @@
+{
+    "svdb query": {
+        "content": [
+            "test_query.vcf",
+            "versions.yml"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2023-11-22T14:56:08.90223505"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svdb/query/tests/tags.yml b/modules/nf-core/svdb/query/tests/tags.yml
new file mode 100644
index 00000000..f4096378
--- /dev/null
+++ b/modules/nf-core/svdb/query/tests/tags.yml
@@ -0,0 +1,2 @@
+svdb/query:
+  - modules/nf-core/svdb/query/**
diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml
index 56cc0fb1..017c259d 100644
--- a/modules/nf-core/tabix/bgzip/environment.yml
+++ b/modules/nf-core/tabix/bgzip/environment.yml
@@ -1,8 +1,7 @@
-name: tabix_bgzip
 channels:
   - conda-forge
   - bioconda
-  - defaults
+
 dependencies:
-  - bioconda::tabix=1.11
   - bioconda::htslib=1.20
+  - bioconda::tabix=1.11
diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml
index 621d49ea..131e92cf 100644
--- a/modules/nf-core/tabix/bgzip/meta.yml
+++ b/modules/nf-core/tabix/bgzip/meta.yml
@@ -13,33 +13,42 @@ tools:
       documentation: http://www.htslib.org/doc/bgzip.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:tabix
 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
+  - - 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: "*."
+      - 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"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${output}.gzi:
+          type: file
+          description: Optional gzip index file for compressed inputs
+          pattern: "*.gzi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml
index b9644de9..017c259d 100644
--- a/modules/nf-core/tabix/bgziptabix/environment.yml
+++ b/modules/nf-core/tabix/bgziptabix/environment.yml
@@ -1,8 +1,7 @@
-name: tabix_bgziptabix
 channels:
   - conda-forge
   - bioconda
-  - defaults
+
 dependencies:
-  - bioconda::tabix=1.11
   - bioconda::htslib=1.20
+  - bioconda::tabix=1.11
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index 05041f49..22f37a77 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def args2 = task.ext.args2 ?: ''
+    def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi"
     """
     echo "" | gzip > ${prefix}.${input.getExtension()}.gz
-    touch ${prefix}.${input.getExtension()}.gz.tbi
-    touch ${prefix}.${input.getExtension()}.gz.csi
+    touch ${prefix}.${input.getExtension()}.gz.${index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
index 438aba4d..806fbc12 100644
--- a/modules/nf-core/tabix/bgziptabix/meta.yml
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -13,38 +13,50 @@ tools:
       documentation: https://www.htslib.org/doc/tabix.1.html
       doi: 10.1093/bioinformatics/btq671
       licence: ["MIT"]
+      identifier: biotools:tabix
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - tab:
-      type: file
-      description: TAB-delimited genome position file
-      pattern: "*.{bed,gff,sam,vcf}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: Sorted tab-delimited genome file
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - gz:
-      type: file
-      description: Output compressed file
-      pattern: "*.{gz}"
-  - tbi:
-      type: file
-      description: tabix index file
-      pattern: "*.{gz.tbi}"
-  - csi:
-      type: file
-      description: tabix alternate index file
-      pattern: "*.{gz.csi}"
+  - gz_tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gz":
+          type: file
+          description: bgzipped tab-delimited genome file
+          pattern: "*.gz"
+      - "*.tbi":
+          type: file
+          description: tabix index file
+          pattern: "*.tbi"
+  - gz_csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gz":
+          type: file
+          description: bgzipped tab-delimited genome file
+          pattern: "*.gz"
+      - "*.csi":
+          type: file
+          description: csi index file
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@maxulysse"
   - "@DLBPointon"
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
index 1a84d74f..4d4130dc 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
@@ -91,4 +91,33 @@ nextflow_process {
 
     }
 
+    test("sarscov2_bed_tbi_stub") {
+        config "./tabix_tbi.config"
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/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_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
index c166ea72..fb87799b 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -91,6 +91,47 @@
         },
         "timestamp": "2024-02-19T14:51:00.548801"
     },
+    "sarscov2_bed_tbi_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
+                ],
+                "gz_csi": [
+                    
+                ],
+                "gz_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-25T14:45:18.533169949"
+    },
     "csi_stub": {
         "content": [
             "test.bed.gz"
@@ -101,6 +142,16 @@
         },
         "timestamp": "2024-02-19T14:51:09.218454"
     },
+    "tbi_stub": {
+        "content": [
+            "test.bed.gz"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-25T14:45:18.550930179"
+    },
     "tbi_test": {
         "content": [
             "tbi_test.bed.gz"
@@ -115,13 +166,7 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
                     [
@@ -145,13 +190,7 @@
                     ]
                 ],
                 "gz_tbi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
@@ -159,9 +198,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-19T11:29:45.105209991"
+        "timestamp": "2024-09-25T14:44:19.786135972"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
index 4d1f9dd4..017c259d 100644
--- a/modules/nf-core/tabix/tabix/environment.yml
+++ b/modules/nf-core/tabix/tabix/environment.yml
@@ -1,9 +1,6 @@
-name: tabix_tabix
-
 channels:
   - conda-forge
   - bioconda
-  - defaults
 
 dependencies:
   - bioconda::htslib=1.20
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index ae5b4f43..7864832d 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -11,34 +11,43 @@ tools:
       documentation: https://www.htslib.org/doc/tabix.1.html
       doi: 10.1093/bioinformatics/btq671
       licence: ["MIT"]
+      identifier: biotools:tabix
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - tab:
-      type: file
-      description: TAB-delimited genome position file compressed with bgzip
-      pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - tab:
+        type: file
+        description: TAB-delimited genome position file compressed with bgzip
+        pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - tbi:
-      type: file
-      description: tabix index file
-      pattern: "*.{tbi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: tabix index file
+          pattern: "*.{tbi}"
   - csi:
-      type: file
-      description: coordinate sorted index file
-      pattern: "*.{csi}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: coordinate sorted index file
+          pattern: "*.{csi}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml
new file mode 100644
index 00000000..721e0df3
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::trgt=1.2.0"
diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf
new file mode 100644
index 00000000..3fa0b7b4
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/main.nf
@@ -0,0 +1,56 @@
+process TRGT_GENOTYPE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
+        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta) , path(bam), path(bai), val(karyotype)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(repeats)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")      , emit: vcf
+    tuple val(meta), path("*.spanning.bam"), emit: bam     , optional: true
+    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 karyo = karyotype ? "--karyotype ${karyotype}" : ""
+    """
+    trgt genotype \\
+        $args \\
+        --genome ${fasta} \\
+        --reads ${bam} \\
+        --repeats ${repeats} \\
+        ${karyo} \\
+        --threads ${task.cpus} \\
+        --output-prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.spanning.bam
+    echo "" | gzip > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/trgt/genotype/meta.yml b/modules/nf-core/trgt/genotype/meta.yml
new file mode 100644
index 00000000..bd17e4ca
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/meta.yml
@@ -0,0 +1,98 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "trgt_genotype"
+description: Tandem repeat genotyping from PacBio HiFi data
+keywords:
+  - repeat expansion
+  - pacbio
+  - genomics
+tools:
+  - "trgt":
+      description: "Tandem repeat genotyping and visualization from PacBio HiFi data"
+      homepage: "https://github.com/PacificBiosciences/trgt"
+      documentation: "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md"
+      tool_dev_url: "https://github.com/PacificBiosciences/trgt"
+      doi: "10.1038/s41587-023-02057-3"
+      licence:
+        ["Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: "Index of the BAM file"
+        pattern: "*.bam"
+    - karyotype:
+        type: string
+        description: "Karyotype of the sample. Either XX or XY. Defaults to XX if not given"
+        enum:
+          - XX
+          - XY
+  - - meta2:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fasta:
+        type: file
+        description: "FASTA reference file"
+        pattern: "*.{fasta,fa,fna}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fai:
+        type: file
+        description: "Index for FASTA file"
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy map containing repeat information
+          e.g. `[ id: 'repeats' ]`
+    - repeats:
+        type: file
+        description: "BED file with repeat coordinates"
+        pattern: "*.bed"
+
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: "VCF file with repeat genotypes"
+          pattern: "*.vcf.gz"
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.spanning.bam":
+          type: file
+          description: BAM file with pieces of reads aligning to repeats
+          pattern: "*.spanning.bam"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@Schmytzi"
+  - "@fellen31"
+maintainers:
+  - "@Schmytzi"
diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test b/modules/nf-core/trgt/genotype/tests/main.nf.test
new file mode 100644
index 00000000..d93a2e96
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/tests/main.nf.test
@@ -0,0 +1,154 @@
+// nf-core modules test trgt
+nextflow_process {
+
+    name "Test Process TRGT_GENOTYPE"
+    script "../main.nf"
+    process "TRGT_GENOTYPE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "trgt"
+    tag "trgt/genotype"
+    tag "samtools/faidx"
+    tag "gunzip"
+
+    setup {
+        run("GUNZIP"){
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id : 'chr22' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true)
+                ]
+            """
+            }
+        }
+        run("SAMTOOLS_FAIDX"){
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+    }
+
+    test("homo sapiens - [bam,bai,XX], [fa,fai], bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,[]], [fa,fai], bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,XX], [fa,fai], bed - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                                .collectFile(name : 'repeats.bed', newLine: false)
+                                .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,[]], [fa,fai], bed - stub") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test.snap b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap
new file mode 100644
index 00000000..9e50fb81
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap
@@ -0,0 +1,198 @@
+{
+    "homo sapiens - [bam,bai,XX], [fa,fai], bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:07:55.029938504"
+    },
+    "homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:08:33.937952067"
+    },
+    "homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:16:39.197756426"
+    },
+    "homo sapiens - [bam,bai,[]], [fa,fai], bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:08:07.631383773"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/trgt/merge/environment.yml b/modules/nf-core/trgt/merge/environment.yml
new file mode 100644
index 00000000..614dc872
--- /dev/null
+++ b/modules/nf-core/trgt/merge/environment.yml
@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::trgt=1.2.0"
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/trgt/merge/main.nf
similarity index 55%
rename from modules/nf-core/bcftools/merge/main.nf
rename to modules/nf-core/trgt/merge/main.nf
index 41dc1a0d..73e51b02 100644
--- a/modules/nf-core/bcftools/merge/main.nf
+++ b/modules/nf-core/trgt/merge/main.nf
@@ -1,64 +1,63 @@
-process BCFTOOLS_MERGE {
+process TRGT_MERGE {
     tag "$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:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
+        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
 
     input:
-    tuple val(meta), path(vcfs), path(tbis)
-    tuple val(meta2), path(fasta)
-    tuple val(meta3), path(fai)
-    path(bed)
+    tuple val(meta) , path(vcfs), path(tbis)
+    tuple val(meta2), path(fasta) // optional
+    tuple val(meta3), path(fai)   // optional
 
     output:
-    tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: merged_variants
-    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
 
     script:
-    def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
-
-    def regions = bed ? "--regions-file $bed" : ""
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${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"
+    def output = args.contains("--output ") || args.contains("--output=") || args.contains("-o ") ? "" : "--output ${prefix}.${extension}"
+    def reference = fasta ? "--genome ${fasta}" : ""
 
     """
-    bcftools merge \\
+    trgt merge \\
         $args \\
-        $regions \\
-        --threads $task.cpus \\
-        --output ${prefix}.${extension} \\
-        $vcfs
+        $reference \\
+        $output \\
+        --vcf ${vcfs}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args   ?: ''
+    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"
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${extension}
+    $create_cmd ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/trgt/merge/meta.yml b/modules/nf-core/trgt/merge/meta.yml
new file mode 100644
index 00000000..e8b79cb2
--- /dev/null
+++ b/modules/nf-core/trgt/merge/meta.yml
@@ -0,0 +1,80 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "trgt_merge"
+description: Merge TRGT VCFs from multiple samples
+keywords:
+  - trgt
+  - repeat expansion
+  - pacbio
+  - genomics
+tools:
+  - "trgt":
+      description: "Tandem repeat genotyping and visualization from PacBio HiFi data"
+      homepage: "https://github.com/PacificBiosciences/trgt"
+      documentation: "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md"
+      tool_dev_url: "https://github.com/PacificBiosciences/trgt"
+      doi: "10.1038/s41587-023-02057-3"
+      licence:
+        ["Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - vcfs:
+        type: file
+        description: |
+          List containing VCF files from TRGT
+          Must contain at least 2 elements unless `--force-single` is given
+          Samples in each VCf must be pairwise disjoint
+    - tbis:
+        type: file
+        description: |
+          List containing indexes of VCF files from TRGT
+          Must contain at least 2 elements unless `--force-single` is given
+  - - meta2:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fasta:
+        type: file
+        description: |
+          FASTA reference file (optional)
+          Required if VCFs were generated with TRGT pre 1.0
+        pattern: "*.{fasta,fa,fna}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fai:
+        type: file
+        description: |
+          Index for FASTA file (optional)
+          Required if VCFs were generated with TRGT pre 1.0
+        pattern: "*.fai"
+
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+          type: file
+          description: "Merged output file"
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@Schmytzi"
+maintainers:
+  - "@Schmytzi"
diff --git a/modules/nf-core/trgt/merge/tests/main.nf.test b/modules/nf-core/trgt/merge/tests/main.nf.test
new file mode 100644
index 00000000..dfccd4f9
--- /dev/null
+++ b/modules/nf-core/trgt/merge/tests/main.nf.test
@@ -0,0 +1,193 @@
+// nf-core modules test trgt/merge
+nextflow_process {
+
+    name "Test Process TRGT_MERGE"
+    script "../main.nf"
+    process "TRGT_MERGE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "trgt"
+    tag "trgt/merge"
+    tag "trgt/genotype"
+    tag "samtools/faidx"
+    tag "samtools/sort"
+    tag "samtools/index"
+    tag "bcftools/sort"
+    tag "gunzip"
+
+    setup {
+        run("GUNZIP"){
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id : 'chr22' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        run("SAMTOOLS_FAIDX"){
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+        run("TRGT_GENOTYPE"){
+            script "../../genotype/main.nf"
+            process {
+                """
+                input[0] = Channel.fromList([
+                    tuple(
+                        [ id:'test1' ],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                        'XX'
+                    ),
+                    tuple(
+                        [ id:'test2' ],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                        'XX'
+                    )
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                            .first()
+                """
+            }
+        }
+        run("BCFTOOLS_SORT"){
+            script "../../../bcftools/sort/main.nf"
+            process {
+                """
+                input[0] = TRGT_GENOTYPE.out.vcf
+                """
+            }
+        }
+    }
+    test("homo sapiens - 2 VCFs") {
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_SORT.out.vcf
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
+                            .groupTuple()
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    test("homo sapiens - 2 VCFs - reference") {
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_SORT.out.vcf
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
+                            .groupTuple()
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    test("homo sapiens - 1 VCF") {
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_SORT.out.vcf
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .first()
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert !process.success }
+            )
+        }
+    }
+    test("homo sapiens - 1 VCF - --force-single") {
+        when {
+            params {
+                trgt_merge_args = "--force-single"
+            }
+            process {
+                """
+                input[0] = BCFTOOLS_SORT.out.vcf
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .first()
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.sampleCount,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    test("homo sapiens - 2 VCFs - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_SORT.out.vcf
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .map { meta, vcf, tbi -> [ [ id : 'test' ], vcf, tbi ] }
+                            .groupTuple()
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/trgt/merge/tests/main.nf.test.snap b/modules/nf-core/trgt/merge/tests/main.nf.test.snap
new file mode 100644
index 00000000..73f306b0
--- /dev/null
+++ b/modules/nf-core/trgt/merge/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "homo sapiens - 2 VCFs - reference": {
+        "content": [
+            "75acbf6205a44ca44d6fc644dda57d82",
+            "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]",
+            2,
+            [
+                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T14:52:26.329527707"
+    },
+    "homo sapiens - 2 VCFs": {
+        "content": [
+            "75acbf6205a44ca44d6fc644dda57d82",
+            "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]",
+            2,
+            [
+                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T14:39:54.475134386"
+    },
+    "homo sapiens - 2 VCFs - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T15:06:23.198648143"
+    },
+    "homo sapiens - 1 VCF - --force-single": {
+        "content": [
+            "6e09773892c37f17e01c9771e8ef2171",
+            "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
+            1,
+            [
+                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T15:01:59.765895584"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/trgt/merge/tests/nextflow.config b/modules/nf-core/trgt/merge/tests/nextflow.config
new file mode 100644
index 00000000..b5caec9f
--- /dev/null
+++ b/modules/nf-core/trgt/merge/tests/nextflow.config
@@ -0,0 +1,15 @@
+params {
+    trgt_merge_args = ""
+}
+process {
+    withName: "BCFTOOLS_SORT" {
+        ext.args = "--write-index=tbi --output-type z"
+        ext.prefix = { "sorted_${meta.id}" }
+    }
+    withName: "TRGT_GENOTYPE" {
+        ext.args = { "--sample-name ${meta.id}"}
+    }
+    withName: "TRGT_MERGE" {
+        ext.args = params.trgt_merge_args
+    }
+}
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index 4f498244..c7794856 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,8 +1,6 @@
-name: untar
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::grep=3.11
   - conda-forge::sed=4.8
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 9bd8f554..867f56ea 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -11,8 +11,8 @@ process UNTAR {
     tuple val(meta), path(archive)
 
     output:
-    tuple val(meta), path("$prefix"), emit: untar
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path("$dir"), emit: untar
+    path "versions.yml"          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,9 +21,9 @@ process UNTAR {
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
-
+    dir = prefix.split('/')[1]
     """
-    mkdir $prefix
+    mkdir -p $prefix
 
     ## Ensures --strip-components only applied when top level of tar contents is a directory
     ## If just files or multiple directories, place all in prefix
@@ -51,8 +51,9 @@ process UNTAR {
 
     stub:
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
+    dir = prefix.split('/')[1]
     """
-    mkdir ${prefix}
+    mkdir -p ${prefix}
     ## Dry-run untaring the archive to get the files and place all in prefix
     if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
         for i in `tar -tf ${archive}`;
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index a9a2110f..290346b3 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -10,30 +10,33 @@ tools:
         Extract tar.gz files.
       documentation: https://www.gnu.org/software/tar/manual/
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - archive:
-      type: file
-      description: File to be untar
-      pattern: "*.{tar}.{gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - archive:
+        type: file
+        description: File to be untar
+        pattern: "*.{tar}.{gz}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - untar:
-      type: directory
-      description: Directory containing contents of archive
-      pattern: "*/"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - $prefix:
+          type: directory
+          description: Directory containing contents of archive
+          pattern: "*/"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/untar/untar.diff b/modules/nf-core/untar/untar.diff
new file mode 100644
index 00000000..2f1c8b6d
--- /dev/null
+++ b/modules/nf-core/untar/untar.diff
@@ -0,0 +1,45 @@
+Changes in module 'nf-core/untar'
+'modules/nf-core/untar/meta.yml' is unchanged
+Changes in 'untar/main.nf':
+--- modules/nf-core/untar/main.nf
++++ modules/nf-core/untar/main.nf
+@@ -11,8 +11,8 @@
+     tuple val(meta), path(archive)
+ 
+     output:
+-    tuple val(meta), path("$prefix"), emit: untar
+-    path "versions.yml"             , emit: versions
++    tuple val(meta), path("$dir"), emit: untar
++    path "versions.yml"          , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -21,9 +21,9 @@
+     def args  = task.ext.args ?: ''
+     def args2 = task.ext.args2 ?: ''
+     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
+-
++    dir = prefix.split('/')[1]
+     """
+-    mkdir $prefix
++    mkdir -p $prefix
+ 
+     ## Ensures --strip-components only applied when top level of tar contents is a directory
+     ## If just files or multiple directories, place all in prefix
+@@ -51,8 +51,9 @@
+ 
+     stub:
+     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
++    dir = prefix.split('/')[1]
+     """
+-    mkdir ${prefix}
++    mkdir -p ${prefix}
+     ## Dry-run untaring the archive to get the files and place all in prefix
+     if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+         for i in `tar -tf ${archive}`;
+
+'modules/nf-core/untar/environment.yml' is unchanged
+'modules/nf-core/untar/tests/tags.yml' is unchanged
+'modules/nf-core/untar/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/untar/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/nextflow.config b/nextflow.config
index 3551d731..5dd6f78f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,64 +10,74 @@
 params {
 
     // Input options
-    input                      = null
-    bed                        = null
-    cadd_resources             = null
-    cadd_prescored             = null
-    par_regions                = null
-    tandem_repeats             = null
-    trgt_repeats               = null
-    variant_catalog            = null
-    reduced_penetrance         = null
-    score_config_snv           = null
-    snp_db                     = null
-    variant_consequences_snv   = null
-    vep_cache                  = null
-    vep_plugin_files           = null
-    hificnv_xy                 = null
-    hificnv_xx                 = null
-    hificnv_exclude            = null
-    somalier_sites             = null
-    deepvariant_model_type     = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO'
+    input                        = null
+    target_regions               = null
+    cadd_resources               = null
+    cadd_prescored_indels        = null
+    filter_variants_hgnc_ids     = null
+    par_regions                  = null
+    tandem_repeats               = null
+    trgt_repeats                 = null
+    stranger_repeat_catalog      = null
+    genmod_reduced_penetrance    = null
+    genmod_score_config_snvs     = null
+    genmod_score_config_svs      = null
+    echtvar_snv_databases        = null
+    svdb_sv_databases            = null
+    variant_consequences_snvs    = null
+    variant_consequences_svs     = null
+    vep_cache                    = null
+    vep_plugin_files             = null
+    hificnv_expected_xy_cn       = null
+    hificnv_expected_xx_cn       = null
+    hificnv_excluded_regions     = null
+    somalier_sites               = null
 
     // Skip parts of the workflow
-    skip_aligned_read_qc       = false
-    skip_raw_read_qc           = false
-    skip_assembly_wf           = params.preset == 'ONT_R10' ? true : false
-    skip_mapping_wf            = false
-    skip_methylation_wf        = params.preset == 'pacbio' ? true : false
-    skip_rank_variants         = false
-    skip_repeat_calling        = params.preset == 'ONT_R10' ? true : false
-    skip_repeat_annotation     = params.preset == 'ONT_R10' ? true : false
-    skip_phasing_wf            = false
-    skip_short_variant_calling = false
-    skip_snv_annotation        = false
-    skip_cnv_calling           = false
-    skip_call_paralogs         = false
+    skip_genome_assembly         = params.preset == 'ONT_R10' ? true : false
+    skip_call_paralogs           = false
+    skip_cnv_calling             = false
+    skip_alignment               = false
+    skip_methylation_pileups     = params.preset == 'pacbio' ? true : false
+    skip_phasing                 = false
+    skip_qc                      = false
+    skip_rank_variants           = false
+    skip_repeat_calling          = params.preset == 'ONT_R10' ? true : false
+    skip_repeat_annotation       = params.preset == 'ONT_R10' ? true : false
+    skip_snv_calling             = false
+    skip_snv_annotation          = false
+    skip_sv_annotation           = false
 
-    preset                     = 'revio'
-    variant_caller             = 'deepvariant'
-    phaser                     = 'whatshap'
-    hifiasm_mode               = 'hifi-only'
+    deepvariant_model_type       = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO'
+    minimap2_read_mapping_preset = params.preset == 'ONT_R10' ? 'lr:hq' : 'map-hifi'
+    filter_snvs_expression       = ''
+    filter_svs_expression        = ''
+    phaser                       = 'longphase'
+    sv_caller                    = 'severus'
+    preset                       = 'revio'
+    hifiasm_mode                 = 'hifi-only'
+    snv_caller                   = 'deepvariant'
+    vep_cache_version            = 110
 
-    vep_cache_version          = 110
+    // Test config options
+    extra_modkit_options         = ''
+    extra_vep_options            = ''
+    extra_paraphase_options      = ''
+    extra_hifiasm_options        = ''
 
     // Preprocessing/parallelisation
-    parallel_snv               = 13
-    parallel_alignments         = 1
+    snv_calling_processes        = 13
+    alignment_processes          = 8
 
     // References
-    fasta                      = null
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes'
-    igenomes_ignore            = true
+    fasta                        = null
 
     // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
-    max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    multiqc_config               = null
+    multiqc_title                = null
+    multiqc_logo                 = null
+    max_multiqc_email_size       = '25.MB'
+    multiqc_methods_description  = null
 
     // Boilerplate options
     outdir                       = null
@@ -77,53 +87,30 @@ params {
     plaintext_email              = false
     monochrome_logs              = false
     hook_url                     = null
-    help                         = false
+
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
 
     // Config options
-    config_profile_name        = null
-    config_profile_description = null
-    custom_config_version      = 'master'
-    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_contact     = null
-    config_profile_url         = null
+    config_profile_name          = null
+    config_profile_description   = null
+
+    custom_config_version        = 'master'
+    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact       = null
+    config_profile_url           = null
 
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-    validationSkipDuplicateCheck     = false
-    validationS3PathCheck            = false
-    monochromeLogs                   = false
+    validate_params              = true
+
 }
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load genomic-medicine-sweden/nallo custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-//try {
-//    includeConfig "${params.custom_config_base}/pipeline/nallo.config"
-//} catch (Exception e) {
-//    System.err.println("WARNING: Could not load nf-core/config/nallo profiles: ${params.custom_config_base}/pipeline/nallo.config")
-//}
-
 profiles {
     debug {
         dumpHashes              = true
@@ -138,7 +125,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -227,25 +214,18 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -257,8 +237,15 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = """\
+bash
+
+set -e # Exit if a tool returns a non-zero status/exit code
+set -u # Treat unset variables and parameters as an error
+set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+set -C # No clobber - prevent output redirection from overwriting files.
+"""
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -287,9 +274,45 @@ manifest {
     homePage        = 'https://github.com/genomic-medicine-sweden/nallo'
     description     = """Long-read variant calling pipeline"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
-    version         = '0.3.1'
-    doi             = ''
+    nextflowVersion = '!>=24.04.2'
+    version         = '0.4.0'
+    doi             = '10.5281/zenodo.13748210'
+}
+
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    defaultIgnoreParams = ["genomes"]
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+\033[0;34m                                   _                              _ _      _
+\033[0;34m   __ _  ___ _ __   ___  _ __ ___ (_) ___      _ __ ___   ___  __| (_) ___(_)_ __   ___
+\033[0;34m  / _` |/ _ \\ '_ \\ / _ \\| '_ ` _ \\| |/ __|____| '_ ` _ \\ / _ \\/ _` | |/ __| | '_ \\ / _ \\_____
+\033[0;34m | (_| |  __/ | | | (_) | | | | | | | (_|_____| | | | | |  __/ (_| | | (__| | | | |  __/_____|
+\033[0;34m  \\__, |\\___|_| |_|\\___/|_| |_| |_|_|\\___|    |_| |_| |_|\\___|\\__,_|_|\\___|_|_| |_|\\___|
+\033[0;34m  |___/      _____  __| | ___ _ __    / / __   __ _| | | ___
+\033[0;34m / __\\ \\ /\\ / / _ \\/ _` |/ _ \\ '_ \\  / / '_ \\ / _` | | |/ _ \\
+\033[0;34m \\__ \\\\ V  V /  __/ (_| |  __/ | | |/ /| | | | (_| | | | (_) |
+\033[0;34m |___/ \\_/\\_/ \\___|\\__,_|\\___|_| |_/_/ |_| |_|\\__,_|_|_|\\___/
+\033[0;34m
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies\n  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
+    }
 }
 
 // Load modules.config for DSL2 module specific options
@@ -297,11 +320,15 @@ includeConfig 'conf/base.config'
 includeConfig 'conf/modules/annotate_cadd.config'
 includeConfig 'conf/modules/annotate_consequence_pli.config'
 includeConfig 'conf/modules/annotate_repeat_expansions.config'
+includeConfig 'conf/modules/annotate_svs.config'
 includeConfig 'conf/modules/general.config'
 includeConfig 'conf/modules/bam_infer_sex.config'
+includeConfig 'conf/modules/call_cnvs.config'
 includeConfig 'conf/modules/call_paralogs.config'
 includeConfig 'conf/modules/call_repeat_expansions.config'
+includeConfig 'conf/modules/call_svs.config'
 includeConfig 'conf/modules/convert_input_files.config'
+includeConfig 'conf/modules/filter_variants.config'
 includeConfig 'conf/modules/assembly_variant_calling.config'
 includeConfig 'conf/modules/genome_assembly.config'
 includeConfig 'conf/modules/methylation.config'
@@ -312,39 +339,4 @@ includeConfig 'conf/modules/scatter_genome.config'
 includeConfig 'conf/modules/rank_variants.config'
 includeConfig 'conf/modules/short_variant_calling.config'
 includeConfig 'conf/modules/snv_annotation.config'
-includeConfig 'conf/modules/structural_variant_calling.config'
 includeConfig 'conf/modules/short_variant_calling.config'
-includeConfig 'conf/modules/cnv.config'
-
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
-    }
-}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 40f4005b..f283d38f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,47 +1,41 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/nextflow_schema.json",
     "title": "genomic-medicine-sweden/nallo pipeline parameters",
     "description": "Long-read variant calling pipeline",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "workflow_skip_options": {
             "title": "Workflow skip options",
             "type": "object",
             "description": "Allows skipping certain parts of the pipeline",
             "default": "",
             "properties": {
-                "skip_aligned_read_qc": {
+                "skip_qc": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip QC of aligned reads",
+                    "description": "Skip QC of reads",
                     "default": false
                 },
-                "skip_raw_read_qc": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip QC of unaligned (raw) reads",
-                    "default": false
-                },
-                "skip_short_variant_calling": {
+                "skip_snv_calling": {
                     "type": "boolean",
                     "description": "Skip short variant calling",
                     "fa_icon": "fas fa-fast-forward",
                     "default": false
                 },
-                "skip_assembly_wf": {
+                "skip_genome_assembly": {
                     "type": "boolean",
                     "description": "Skip genome assembly and assembly variant calling",
                     "fa_icon": "fas fa-fast-forward",
                     "default": false
                 },
-                "skip_mapping_wf": {
+                "skip_alignment": {
                     "type": "boolean",
                     "description": "Skip read mapping (alignment)",
                     "fa_icon": "fas fa-fast-forward",
                     "default": false
                 },
-                "skip_methylation_wf": {
+                "skip_methylation_pileups": {
                     "type": "boolean",
                     "description": "Skip generation of methylation pileups",
                     "fa_icon": "fas fa-fast-forward",
@@ -59,7 +53,7 @@
                     "fa_icon": "fas fa-fast-forward",
                     "default": false
                 },
-                "skip_phasing_wf": {
+                "skip_phasing": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
                     "description": "Skip phasing of variants and haplotagging of reads",
@@ -70,6 +64,11 @@
                     "description": "Skip short variant annotation",
                     "default": false
                 },
+                "skip_sv_annotation": {
+                    "type": "boolean",
+                    "description": "Skip structural variant annotation",
+                    "default": false
+                },
                 "skip_cnv_calling": {
                     "type": "boolean",
                     "description": "Skip CNV calling",
@@ -123,6 +122,143 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
+                },
+                "cadd_prescored_indels": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "directory-path",
+                    "fa_icon": "fas fa-file",
+                    "description": "Path to a directory containing prescored indels for CADD.",
+                    "help_text": "This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
+                },
+                "cadd_resources": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "directory-path",
+                    "fa_icon": "fas fa-file",
+                    "description": "Path to a directory containing CADD annotations.",
+                    "help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
+                },
+                "par_regions": {
+                    "type": "string",
+                    "description": "Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "tandem_repeats": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "A tandem repeat BED file for sniffles",
+                    "pattern": "^\\S+\\.bed$",
+                    "exists": true
+                },
+                "trgt_repeats": {
+                    "type": "string",
+                    "description": "A BED file with repeats to be genotyped with TRGT",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "echtvar_snv_databases": {
+                    "type": "string",
+                    "pattern": "^\\S+\\.csv$",
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "schema": "/assets/schema_snp_db.json",
+                    "description": "A csv file with echtvar databases to annotate SNVs with",
+                    "exists": true
+                },
+                "svdb_sv_databases": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "file-path",
+                    "description": "Databases used for structural variant annotation in vcf format.",
+                    "fa_icon": "fas fa-file-csv",
+                    "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation.",
+                    "pattern": "^\\S+\\.csv$",
+                    "mimetype": "text/csv",
+                    "schema": "assets/svdb_query_vcf_schema.json"
+                },
+                "stranger_repeat_catalog": {
+                    "type": "string",
+                    "description": "A variant catalog json-file for stranger",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "variant_consequences_snvs": {
+                    "type": "string",
+                    "description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "variant_consequences_svs": {
+                    "type": "string",
+                    "description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "vep_cache": {
+                    "type": "string",
+                    "description": "A path to the VEP cache location",
+                    "format": "path",
+                    "exists": true
+                },
+                "target_regions": {
+                    "type": "string",
+                    "pattern": "^\\S+\\.bed$",
+                    "format": "file-path",
+                    "description": "A BED file with regions of interest, used to limit variant calling.",
+                    "exists": true
+                },
+                "hificnv_expected_xy_cn": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "A BED file containing expected copy number regions for XY samples.",
+                    "exists": true
+                },
+                "hificnv_expected_xx_cn": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "A BED file containing expected copy number regions for XX samples.",
+                    "exists": true
+                },
+                "hificnv_excluded_regions": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "A BED file specifying regions to exclude with HiFiCNV, such as centromeres.",
+                    "exists": true
+                },
+                "genmod_reduced_penetrance": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file-csv",
+                    "description": "A file with gene ids that have reduced penetrance. For use with genmod."
+                },
+                "genmod_score_config_snvs": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "description": "A SNV rank model config file for genmod."
+                },
+                "genmod_score_config_svs": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "description": "A SV rank model config file for genmod."
+                },
+                "somalier_sites": {
+                    "type": "string",
+                    "pattern": "^\\S+\\.vcf(\\.gz)?$",
+                    "description": "A VCF of known polymorphic sites for somalier",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/",
+                    "hidden": true
                 }
             }
         },
@@ -138,19 +274,6 @@
                     "pattern": "^.*\\.(fasta|fa|fna)(\\.gz)?$",
                     "format": "file-path",
                     "exists": true
-                },
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
-                },
-                "igenomes_ignore": {
-                    "type": "boolean",
-                    "description": "Do not load the iGenomes reference config.",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.",
-                    "default": true
                 }
             }
         },
@@ -202,41 +325,6 @@
                 }
             }
         },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -244,12 +332,6 @@
             "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.",
@@ -324,28 +406,6 @@
                     "default": true,
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
-                },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationSkipDuplicateCheck": {
-                    "type": "boolean",
-                    "hidden": true,
-                    "description": "nf-validation related parameter"
-                },
-                "validationS3PathCheck": {
-                    "type": "boolean",
-                    "hidden": true,
-                    "description": "Boolean whether to validate validate AWS S3 paths"
-                },
-                "monochromeLogs": {
-                    "type": "boolean",
-                    "hidden": true,
-                    "description": "Boolean whether to color nf-validation logs"
                 }
             }
         },
@@ -361,17 +421,23 @@
                     "description": "Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`)",
                     "enum": ["revio", "pacbio", "ONT_R10"]
                 },
-                "variant_caller": {
+                "snv_caller": {
                     "type": "string",
                     "default": "deepvariant",
                     "description": "Which short variant software to use (`deepvariant`)",
                     "enum": ["deepvariant"]
                 },
+                "sv_caller": {
+                    "type": "string",
+                    "default": "severus",
+                    "description": "Which structural variant caller to use (`severus`, `sniffles`)",
+                    "enum": ["severus", "sniffles"]
+                },
                 "phaser": {
                     "type": "string",
-                    "default": "whatshap",
-                    "description": "Which phasing software to use (`whatshap`, `hiphase_snv`, `hiphase_sv`)",
-                    "enum": ["whatshap", "hiphase_snv", "hiphase_sv"]
+                    "default": "longphase",
+                    "description": "Which phasing software to use (`longphase`, `whatshap`, `hiphase`)",
+                    "enum": ["longphase", "whatshap", "hiphase"]
                 },
                 "hifiasm_mode": {
                     "type": "string",
@@ -379,16 +445,16 @@
                     "enum": ["hifi-only", "trio-binning"],
                     "default": "hifi-only"
                 },
-                "parallel_alignments": {
+                "alignment_processes": {
                     "type": "integer",
                     "minimum": 1,
-                    "default": 1,
-                    "description": "If parallel_alignments is bigger than 1, input files will be split and aligned in parallel to reduce processing time."
+                    "default": 8,
+                    "description": "If alignment_processes is bigger than 1, input files will be split and aligned in parallel to reduce processing time."
                 },
-                "parallel_snv": {
+                "snv_calling_processes": {
                     "type": "integer",
                     "default": 13,
-                    "description": "If parallel_snv is bigger than 1, short variant calling will be done in parallel to reduce processing time.",
+                    "description": "If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time.",
                     "minimum": 1
                 },
                 "vep_cache_version": {
@@ -399,182 +465,95 @@
                 "vep_plugin_files": {
                     "type": "string",
                     "mimetype": "text/csv",
-                    "description": "A csv file with paths to vep plugin files. pLI and LoFtool are required.",
+                    "description": "A csv file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required.",
                     "schema": "assets/vep_plugin_files_schema.json"
                 },
-                "deepvariant_model_type": {
-                    "type": "string",
-                    "default": "PACBIO",
-                    "description": "Sets the model type used for DeepVariant. This is set automatically using `--preset` by default.",
-                    "hidden": true,
-                    "enum": ["PACBIO", "ONT_R104"]
-                }
-            },
-            "required": ["preset"]
-        },
-        "file_inputs": {
-            "title": "File inputs",
-            "type": "object",
-            "description": "The different files that are required. Some are only required by certain workflows, see the usage documentation.",
-            "default": "",
-            "fa_icon": "fas fa-copy",
-            "properties": {
-                "cadd_prescored": {
-                    "type": "string",
-                    "exists": true,
-                    "format": "directory-path",
-                    "fa_icon": "fas fa-file",
-                    "description": "Path to a directory containing prescored indels for CADD.",
-                    "help_text": "This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
-                },
-                "cadd_resources": {
-                    "type": "string",
-                    "exists": true,
-                    "format": "directory-path",
-                    "fa_icon": "fas fa-file",
-                    "description": "Path to a directory containing CADD annotations.",
-                    "help_text": "This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation."
-                },
-                "par_regions": {
-                    "type": "string",
-                    "description": "Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant",
-                    "format": "file-path",
-                    "exists": true
-                },
-                "tandem_repeats": {
-                    "type": "string",
-                    "format": "file-path",
-                    "description": "A tandem repeat BED file for sniffles",
-                    "pattern": "^\\S+\\.bed$",
-                    "exists": true
-                },
-                "trgt_repeats": {
-                    "type": "string",
-                    "description": "A BED file with repeats to be genotyped with TRGT",
-                    "format": "file-path",
-                    "exists": true
-                },
-                "snp_db": {
-                    "type": "string",
-                    "pattern": "^\\S+\\.csv$",
-                    "format": "file-path",
-                    "mimetype": "text/csv",
-                    "schema": "/assets/schema_snpdb.json",
-                    "description": "A csv file with echtvar databases to annotate SNVs with",
-                    "exists": true
-                },
-                "variant_catalog": {
+                "filter_variants_hgnc_ids": {
                     "type": "string",
-                    "description": "A variant catalog json-file for stranger",
+                    "pattern": "^\\S+\\.(csv|tsv)$",
+                    "description": "A tsv/csv file with a `hgnc_ids` column header, and then one numerical HGNC ID per row. E.g. `4281` or `HGNC:4281`.",
                     "format": "file-path",
-                    "exists": true
-                },
-                "variant_consequences_snv": {
-                    "type": "string",
-                    "description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs.",
-                    "help_text": "For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html",
-                    "fa_icon": "fas fa-file-csv"
+                    "exits": true,
+                    "schema": "assets/schema_hgnc_ids.json"
                 },
-                "vep_cache": {
+                "filter_snvs_expression": {
                     "type": "string",
-                    "description": "A path to the VEP cache location",
-                    "format": "path",
-                    "exists": true
+                    "default": "",
+                    "description": "An expression that is passed to bcftools view to filter SNVs, e.g. --filter_snvs_expression \"-e 'INFO/AQ>60'\""
                 },
-                "bed": {
+                "filter_svs_expression": {
                     "type": "string",
-                    "pattern": "^\\S+\\.bed$",
-                    "format": "file-path",
-                    "description": "A BED file with regions of interest, used to limit short variant calling.",
-                    "exists": true
+                    "default": "",
+                    "description": "An expression that is passed to bcftools view to filter SVs, e.g. --filter_svs_expression \"-e 'INFO/AQ>60'\""
                 },
-                "hificnv_xy": {
-                    "type": "string",
-                    "format": "file-path",
-                    "description": "A BED file containing expected copy number regions for XY samples.",
-                    "exists": true
-                },
-                "hificnv_xx": {
-                    "type": "string",
-                    "format": "file-path",
-                    "description": "A BED file containing expected copy number regions for XX samples.",
-                    "exists": true
-                },
-                "hificnv_exclude": {
+                "deepvariant_model_type": {
                     "type": "string",
-                    "format": "file-path",
-                    "description": "A BED file specifying regions to exclude with HiFiCNV, such as centromeres.",
-                    "exists": true
+                    "default": "PACBIO",
+                    "description": "Sets the model type used for DeepVariant. This is set automatically using `--preset` by default.",
+                    "hidden": true,
+                    "enum": ["PACBIO", "ONT_R104"]
                 },
-                "reduced_penetrance": {
+                "minimap2_read_mapping_preset": {
                     "type": "string",
-                    "exists": true,
-                    "format": "path",
-                    "fa_icon": "fas fa-file-csv",
-                    "description": "A file with gene ids that have reduced penetrance. For use with genmod."
+                    "description": "Sets the minimap2-preset (-x) for read alignment. This is set automatically using the pipeline `--preset` by default.",
+                    "hidden": true,
+                    "enum": ["map-hifi", "map-ont", "lr:hq", "lr:hqae"],
+                    "default": "map-hifi"
                 },
-                "score_config_snv": {
+                "extra_modkit_options": {
                     "type": "string",
-                    "exists": true,
-                    "format": "path",
-                    "fa_icon": "fas fa-file",
-                    "description": "A SNV rank model config file for genmod."
+                    "hidden": true,
+                    "description": "Extra options to modkit, used for test profile."
                 },
-                "somalier_sites": {
+                "extra_vep_options": {
                     "type": "string",
-                    "pattern": "^\\S+\\.vcf(\\.gz)?$",
-                    "description": "A VCF of known polymorphic sites for somalier",
-                    "format": "file-path",
-                    "exists": true
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
                     "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warning."
+                    "description": "Extra options to VEP, used for test profile."
                 },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
+                "extra_paraphase_options": {
+                    "type": "string",
                     "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                    "description": "Extra options to Paraphase, used for test profile."
                 },
-                "pipelines_testdata_base_path": {
+                "extra_hifiasm_options": {
                     "type": "string",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/",
-                    "hidden": true
+                    "hidden": true,
+                    "description": "Extra options to hifiasm, used for test profile."
                 }
-            }
+            },
+            "required": ["preset"]
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/workflow_skip_options"
+            "$ref": "#/$defs/workflow_skip_options"
+        },
+        {
+            "$ref": "#/$defs/input_output_options"
+        },
+        {
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/generic_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/workflow_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/workflow_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/file_inputs"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf-test.config b/nf-test.config
index 67cadb45..7975ed4e 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,13 +1,16 @@
 config {
+    // location for all nf-tests
+    testsDir "."
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "conf/test.config"
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+    // Include plugins
     plugins {
-        load "nft-bam@0.3.0"
-    }
-    stage {
-        copy './nextflow_schema.json'
+        load "nft-bam@0.4.0"
+        load "nft-utils@0.0.3"
+        load "nft-vcf@1.0.7"
     }
-    testsDir "."
-    workDir ".nf-test"
-    configFile "tests/nextflow.config"
-    profile ""
-
 }
diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf
index 9a1dc047..223624a3 100644
--- a/subworkflows/local/annotate_cadd/main.nf
+++ b/subworkflows/local/annotate_cadd/main.nf
@@ -14,12 +14,12 @@ include { TABIX_TABIX as TABIX_CADD            } from '../../../modules/nf-core/
 workflow ANNOTATE_CADD {
 
     take:
-    ch_fai            // channel: [mandatory] [ val(meta), path(fai) ]
-    ch_vcf            // channel: [mandatory] [ val(meta), path(vcfs) ]
-    ch_index          // channel: [mandatory] [ val(meta), path(tbis) ]
-    ch_header         // channel: [mandatory] [ path(txt) ]
-    ch_cadd_resources // channel: [mandatory] [ path(dir) ]
-    ch_cadd_prescored // channel: [mandatory] [ path(dir) ]
+    ch_fai                   // channel: [mandatory] [ val(meta), path(fai) ]
+    ch_vcf                   // channel: [mandatory] [ val(meta), path(vcfs) ]
+    ch_index                 // channel: [mandatory] [ val(meta), path(tbis) ]
+    ch_header                // channel: [mandatory] [ val(meta), path(txt) ]
+    ch_cadd_resources        // channel: [mandatory] [ val(meta), path(dir) ]
+    ch_cadd_prescored_indels // channel: [mandatory] [ val(meta), path(dir) ]
 
     main:
     ch_versions = Channel.empty()
@@ -50,7 +50,7 @@ workflow ANNOTATE_CADD {
     )
     ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions)
 
-    CADD ( BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, ch_cadd_prescored )
+    CADD ( BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, ch_cadd_prescored_indels )
     ch_versions = ch_versions.mix(CADD.out.versions)
 
     TABIX_CADD ( CADD.out.tsv )
@@ -64,7 +64,7 @@ workflow ANNOTATE_CADD {
 
     ANNOTATE_INDELS (
         ch_annotate_indels_in,
-        ch_header,
+        ch_header.map { meta, header -> header },
         CADD_TO_REFERENCE_CHRNAMES.out.output.map { meta, txt -> txt }
     )
     ch_versions = ch_versions.mix(ANNOTATE_INDELS.out.versions)
diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf
index 203a1405..781d5e0f 100644
--- a/subworkflows/local/annotate_consequence_pli.nf
+++ b/subworkflows/local/annotate_consequence_pli.nf
@@ -9,7 +9,7 @@ include { TABIX_BGZIPTABIX    } from '../../modules/nf-core/tabix/bgziptabix/mai
 workflow ANNOTATE_CSQ_PLI {
     take:
     ch_vcf                  // channel: [mandatory] [ val(meta), path(vcf) ]
-    ch_variant_consequences // channel: [mandatory] [ path(consequences) ]
+    ch_variant_consequences // channel: [mandatory] [ val(meta), path(consequences) ]
 
     main:
     ch_versions = Channel.empty()
@@ -24,7 +24,7 @@ workflow ANNOTATE_CSQ_PLI {
     ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
 
     emit:
-    vcf_ann  = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, vcf ] } // channel: [ val(meta), path(vcf) ]
-    tbi_ann  = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, tbi ] } // channel: [ val(meta), path(tbi) ]
-    versions = ch_versions                                                                // channel: [ path(versions.yml) ]
+    vcf      = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> [ meta, vcf ] } // channel: [ val(meta), path(vcf) ]
+    tbi      = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> [ meta, tbi ] } // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions                                                         // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/annotate_repeat_expansions/main.nf b/subworkflows/local/annotate_repeat_expansions/main.nf
index 62b138c6..dc7c5603 100644
--- a/subworkflows/local/annotate_repeat_expansions/main.nf
+++ b/subworkflows/local/annotate_repeat_expansions/main.nf
@@ -7,14 +7,14 @@ include { STRANGER                           } from '../../../modules/nf-core/st
 
 workflow ANNOTATE_REPEAT_EXPANSIONS {
     take:
-    ch_variant_catalog // channel: [mandatory] [ path(variant_catalog.json) ]
-    ch_vcf             // channel: [mandatory] [ val(meta), path(vcf) ]
+    ch_stranger_repeat_catalog // channel: [mandatory] [ path(stranger_repeat_catalog.json) ]
+    ch_vcf                     // channel: [mandatory] [ val(meta), path(vcf) ]
 
     main:
     ch_versions = Channel.empty()
 
     // Annotate, compress and index
-    STRANGER ( ch_vcf, ch_variant_catalog )
+    STRANGER ( ch_vcf, ch_stranger_repeat_catalog )
     ch_versions = ch_versions.mix(STRANGER.out.versions)
 
     COMPRESS_STRANGER (
diff --git a/subworkflows/local/annotate_svs/main.nf b/subworkflows/local/annotate_svs/main.nf
new file mode 100644
index 00000000..14ed7ed7
--- /dev/null
+++ b/subworkflows/local/annotate_svs/main.nf
@@ -0,0 +1,62 @@
+include { SVDB_QUERY                         } from '../../../modules/nf-core/svdb/query/main'
+include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV    } from '../../../modules/nf-core/ensemblvep/vep/main'
+include { TABIX_TABIX as TABIX_ENSEMBLVEP_SV } from '../../../modules/nf-core/tabix/tabix/main'
+
+workflow ANNOTATE_SVS {
+
+    take:
+    ch_vcf                // channel: [mandatory] [ val(meta), path(vcf) ]
+    ch_fasta              // channel: [mandatory] [ val(meta), path(fasta) ]
+    ch_sv_dbs             // channel: [mandatory] [ val(meta), path(csv) ]
+    ch_vep_cache          // channel: [mandatory] [ path(cache) ]
+    val_vep_cache_version //  string: [mandatory] default: 110
+    ch_vep_extra_files    // channel: [mandatory] [ path(files) ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    ch_sv_dbs
+        .map { meta, csv -> csv }
+        .splitCsv ( header:true )
+        .multiMap { row ->
+            vcf_dbs:  row.filename
+            in_frqs:  row.in_freq_info_key
+            in_occs:  row.in_allele_count_info_key
+            out_frqs: row.out_freq_info_key
+            out_occs: row.out_allele_count_info_key
+        }
+        .set { ch_svdb_in }
+
+    // Annotate with SVDB VCF "databases"
+    SVDB_QUERY (
+        ch_vcf,
+        ch_svdb_in.in_occs.toList(),
+        ch_svdb_in.in_frqs.toList(),
+        ch_svdb_in.out_occs.toList(),
+        ch_svdb_in.out_frqs.toList(),
+        ch_svdb_in.vcf_dbs.toList(),
+        []
+        )
+        ch_versions = ch_versions.mix(SVDB_QUERY.out.versions)
+
+    ENSEMBLVEP_SV (
+        SVDB_QUERY.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        "GRCh38",
+        "homo_sapiens",
+        val_vep_cache_version,
+        ch_vep_cache,
+        ch_fasta,
+        ch_vep_extra_files
+    )
+    ch_versions = ch_versions.mix(ENSEMBLVEP_SV.out.versions)
+
+    TABIX_ENSEMBLVEP_SV (
+        ENSEMBLVEP_SV.out.vcf
+    )
+    ch_versions = ch_versions.mix(TABIX_ENSEMBLVEP_SV.out.versions)
+
+    emit:
+    vcf      = ENSEMBLVEP_SV.out.vcf       // channel: [ val(meta), path(vcf) ]
+    tbi      = TABIX_ENSEMBLVEP_SV.out.tbi // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions                 // channel: [ path(versions.yml) ]
+}
diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test b/subworkflows/local/annotate_svs/tests/main.nf.test
new file mode 100644
index 00000000..df7bc027
--- /dev/null
+++ b/subworkflows/local/annotate_svs/tests/main.nf.test
@@ -0,0 +1,115 @@
+nextflow_workflow {
+
+    name "Test Workflow ANNOTATE_SVS"
+    script "../"
+    workflow "ANNOTATE_SVS"
+    config "./nextflow.config"
+
+    setup {
+        run("GUNZIP") {
+            script "../../../../modules/nf-core/gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'hg38' ],
+                    file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        run("SEVERUS") {
+            script "../../../../modules/nf-core/severus/main"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false, project: 'project' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true),
+                    [],
+                    [],
+                    []
+                ]
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        run("UNTAR") {
+            script "../../../../modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'vep_cache' ],
+                    file(params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz', checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+    }
+
+    test("severus, fasta, svdb, vep_cache, '110', vep_plugin_files") {
+
+        when {
+            workflow {
+                """
+                input[0] = SEVERUS.out.all_vcf
+                input[1] = GUNZIP.out.gunzip
+                input[2] = Channel.of([
+                    [ id: 'svdb_sv_databases' ],
+                    file(params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv', checkIfExists: true)
+                ])
+                input[3] = UNTAR.out.untar.map { meta, cache -> cache }
+                input[4] = Channel.value('110')
+                input[5] = Channel.of([
+                    file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.versions,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    file(workflow.out.tbi.get(0).get(1)).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("severus, fasta, svdb, vep_cache, '110', vep_plugin_files -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = SEVERUS.out.all_vcf
+                input[1] = GUNZIP.out.gunzip
+                input[2] = Channel.of([
+                    [ id: 'svdb_sv_databases' ],
+                    file(params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv', checkIfExists: true)
+                ])
+                input[3] = UNTAR.out.untar.map { meta, cache -> cache }
+                input[4] = Channel.value('110')
+                input[5] = Channel.of([
+                    file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out.versions).match() }
+            )
+        }
+
+    }
+}
diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test.snap b/subworkflows/local/annotate_svs/tests/main.nf.test.snap
new file mode 100644
index 00000000..338a454e
--- /dev/null
+++ b/subworkflows/local/annotate_svs/tests/main.nf.test.snap
@@ -0,0 +1,32 @@
+{
+    "severus, fasta, svdb, vep_cache, '110', vep_plugin_files -stub": {
+        "content": [
+            [
+                "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d",
+                "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed",
+                "versions.yml:md5,d2a9a640a711b2d559e13f9bca9d7a3b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-04T16:18:47.369135866"
+    },
+    "severus, fasta, svdb, vep_cache, '110', vep_plugin_files": {
+        "content": [
+            [
+                "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d",
+                "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed",
+                "versions.yml:md5,d2a9a640a711b2d559e13f9bca9d7a3b"
+            ],
+            "28e9be031273d5e4a94a8654da6e56ed",
+            "test_svs_cnvs_merged_annotated.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-04T16:18:35.246526033"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/annotate_svs/tests/nextflow.config b/subworkflows/local/annotate_svs/tests/nextflow.config
new file mode 100644
index 00000000..ee5a33ed
--- /dev/null
+++ b/subworkflows/local/annotate_svs/tests/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+    withName: 'UNTAR' {
+        ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' }
+    }
+
+    withName: 'ANNOTATE_SVS:ENSEMBLVEP_SV' {
+        ext.args = { [
+            '--offline',
+            '--vcf',
+            '--compress_output bgzip'
+        ].join(' ') }
+    }
+    withName: 'CALL_SVS:SVDB_MERGE' {
+        ext.args2 = '--no-version'
+    }
+}
diff --git a/subworkflows/local/call_cnvs/main.nf b/subworkflows/local/call_cnvs/main.nf
new file mode 100644
index 00000000..7407a19a
--- /dev/null
+++ b/subworkflows/local/call_cnvs/main.nf
@@ -0,0 +1,62 @@
+include { ADD_FOUND_IN_TAG } from '../../../modules/local/add_found_in_tag'
+include { HIFICNV          } from '../../../modules/local/pacbio/hificnv'
+include { SVDB_MERGE       } from '../../../modules/nf-core/svdb/merge/main'
+include { TABIX_TABIX      } from '../../../modules/nf-core/tabix/tabix/main'
+
+workflow CALL_CNVS {
+
+    take:
+    ch_bam_bai_vcf     // channel: [ val(meta), path(bam), path(vcf) ]
+    ch_fasta           // channel: [ val(meta), path(fasta) ]
+    ch_expected_xy_bed // channel: [ val(meta), path(bed) ]
+    ch_expected_xx_bed // channel: [ val(meta), path(bed) ]
+    ch_exclude_bed     // channel: [ val(meta), path(bed) ]
+
+    main:
+    ch_versions     = Channel.empty()
+
+    ch_bam_bai_vcf
+        .map { meta, bam, bai, vcf -> [ meta, bam, bai, vcf, meta.sex ] }
+        .set { ch_hificnv_in }
+
+    // Run HiFiCNV
+    HIFICNV (
+        ch_hificnv_in,
+        ch_fasta,
+        ch_expected_xy_bed,
+        ch_expected_xx_bed,
+        ch_exclude_bed
+    )
+    ch_versions = ch_versions.mix(HIFICNV.out.versions)
+
+    // Add FOUND_IN=hificnv to VCF
+    ADD_FOUND_IN_TAG (
+        HIFICNV.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        "hificnv"
+    )
+    ch_versions = ch_versions.mix(ADD_FOUND_IN_TAG.out.versions)
+
+    ADD_FOUND_IN_TAG.out.vcf
+        .map { meta, vcf -> [ [ 'id': meta.family_id ], vcf ] }
+        .groupTuple()
+        .set { svdb_merge_in }
+
+    // Merge the files
+    SVDB_MERGE (
+        svdb_merge_in,
+        [],
+        true
+    )
+    ch_versions = ch_versions.mix(SVDB_MERGE.out.versions)
+
+    TABIX_TABIX ( SVDB_MERGE.out.vcf )
+    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
+
+    emit:
+    sample_vcf  = ADD_FOUND_IN_TAG.out.vcf // channel: [ val(meta), path(vcf) ]
+    sample_tbi  = ADD_FOUND_IN_TAG.out.tbi // channel: [ val(meta), path(tbi) ]
+    family_vcf  = SVDB_MERGE.out.vcf       // channel: [ val(meta), path(vcf) ]
+    family_tbi  = TABIX_TABIX.out.tbi      // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions                 // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/local/call_cnvs/tests/main.nf.test b/subworkflows/local/call_cnvs/tests/main.nf.test
new file mode 100644
index 00000000..3341f7c2
--- /dev/null
+++ b/subworkflows/local/call_cnvs/tests/main.nf.test
@@ -0,0 +1,253 @@
+nextflow_workflow {
+
+    name "Test Workflow CALL_CNVS"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "CALL_CNVS"
+
+    setup {
+        run("GUNZIP") {
+            script "../../../../modules/nf-core/gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+
+        }
+        run("SAMTOOLS_FAIDX") {
+            script "../../../../modules/nf-core/samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+        run("MINIMAP2_ALIGN") {
+            script "../../../../modules/nf-core/minimap2/align/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', family_id: 'test', sex: 1 ],
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true)
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = true
+                input[3] = 'bai'
+                input[4] = false
+                input[5] = false
+                """
+            }
+        }
+        run("DEEPVARIANT_RUNDEEPVARIANT") {
+            script "../../../../modules/nf-core/deepvariant/rundeepvariant/main.nf"
+            process {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .map { meta, bam, bai -> [ meta, bam, bai, file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkIfExists: true) ] }
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+
+    }
+
+    test("1 sample - [bam, bai, [] ], fasta, [], [], [], []") {
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .map { meta, bam, bai -> [ meta, bam, bai, [] ] }
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample - [bam, bai, vcf ], fasta, [], [], [], []") {
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf)
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample - [bam, bai, vcf ], fasta, xy_bed, xx_bed, exclude_bed") {
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf)
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [
+                    [ id: 'xy_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id: 'xx_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id: 'exclude_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/cnv.excluded_regions.hg38.bed.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample - [bam, bai, [] ], fasta, [], [], [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .map { meta, bam, bai -> [ meta, bam, bai, [] ] }
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - [bam, bai, vcf ], fasta, [], [], [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf)
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - [bam, bai, vcf ], fasta, xy_bed, xx_bed, exclude_bed - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf)
+                input[1] = GUNZIP.out.gunzip
+                input[2] = [
+                    [ id: 'xy_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id: 'xx_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id: 'exclude_bed' ],
+                    file(params.pipelines_testdata_base_path + 'reference/cnv.excluded_regions.hg38.bed.gz', checkIfExists: true)
+                ]
+                """
+            }
+            then {
+                assertAll(
+                    { assert workflow.success },
+                    { assert snapshot(workflow.out).match() }
+                )
+            }
+        }
+    }
+}
diff --git a/subworkflows/local/call_cnvs/tests/main.nf.test.snap b/subworkflows/local/call_cnvs/tests/main.nf.test.snap
new file mode 100644
index 00000000..409b8527
--- /dev/null
+++ b/subworkflows/local/call_cnvs/tests/main.nf.test.snap
@@ -0,0 +1,344 @@
+{
+    "1 sample - [bam, bai, vcf ], fasta, [], [], [], [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:44:33.644600302"
+    },
+    "1 sample - [bam, bai, [] ], fasta, [], [], [], [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:44:20.756426372"
+    },
+    "1 sample - [bam, bai, vcf ], fasta, xy_bed, xx_bed, exclude_bed": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]",
+            "444974b6ec3f9600ca12538628e6742c",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]",
+            "171d1b5284a06778c87f54c27ee88bea",
+            [
+                "versions.yml:md5,28a7290514330df198a5df6687535177",
+                "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:44:08.08094773"
+    },
+    "1 sample - [bam, bai, [] ], fasta, [], [], [], []": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=41, phased=false, phasedAutodetect=false]",
+            "576892dd42d2b2cb06542862a4beddc1",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=41, phased=false, phasedAutodetect=false]",
+            "4aaee123cd9279e17220409be6ed7ea3",
+            [
+                "versions.yml:md5,28a7290514330df198a5df6687535177",
+                "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:42:49.173190275"
+    },
+    "1 sample - [bam, bai, vcf ], fasta, xy_bed, xx_bed, exclude_bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "family_id": "test",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,28a7290514330df198a5df6687535177",
+                    "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                    "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                    "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:44:46.71801265"
+    },
+    "1 sample - [bam, bai, vcf ], fasta, [], [], [], []": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=41, phased=false, phasedAutodetect=false]",
+            "576892dd42d2b2cb06542862a4beddc1",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=41, phased=false, phasedAutodetect=false]",
+            "4aaee123cd9279e17220409be6ed7ea3",
+            [
+                "versions.yml:md5,28a7290514330df198a5df6687535177",
+                "versions.yml:md5,98e5fabb16a6a19137277ce414001426",
+                "versions.yml:md5,c22d7e7ddc52579e52ee8ac597b0e829",
+                "versions.yml:md5,fc490a5d4e1a6dce983637532901f1e9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T09:43:28.248043419"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/call_cnvs/tests/nextflow.config b/subworkflows/local/call_cnvs/tests/nextflow.config
new file mode 100644
index 00000000..d5ce57da
--- /dev/null
+++ b/subworkflows/local/call_cnvs/tests/nextflow.config
@@ -0,0 +1,23 @@
+process {
+    withName: 'MINIMAP2_ALIGN' {
+        ext.args = '-x map-hifi'
+    }
+    withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
+        ext.args = '--model_type PACBIO'
+    }
+    withName: 'CALL_CNVS:HIFICNV' {
+        ext.prefix = 'hificnv'
+    }
+    withName: 'CALL_CNVS:SVDB_MERGE' {
+        ext.prefix = 'merged'
+        ext.args2 = '--no-version'
+    }
+    withName: 'CALL_CNVS:ADD_FOUND_IN_TAG' {
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type z',
+            '--write-index=tbi',
+            '--no-version'
+        ].join(' ')
+    }
+}
diff --git a/subworkflows/local/call_paralogs.nf b/subworkflows/local/call_paralogs.nf
index 88c62403..bb4a931d 100644
--- a/subworkflows/local/call_paralogs.nf
+++ b/subworkflows/local/call_paralogs.nf
@@ -1,5 +1,4 @@
-include { PARAPHASE        } from '../../modules/nf-core/paraphase/main'
-include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { PARAPHASE } from '../../modules/nf-core/paraphase/main'
 
 workflow CALL_PARALOGS {
 
@@ -13,19 +12,12 @@ workflow CALL_PARALOGS {
     PARAPHASE ( bam_bai, fasta, [[],[]] )
     ch_versions = ch_versions.mix(PARAPHASE.out.versions)
 
-    PARAPHASE.out.vcf
-        .transpose() // Does create ~160 jobs per sample by default in hg38
-        .set { bgzip_paraphase_vcfs }
-
-    TABIX_BGZIPTABIX ( bgzip_paraphase_vcfs )
-    ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
-
     emit:
-    bam      = PARAPHASE.out.bam           // channel: [ val(meta), bam ]
-    bai      = PARAPHASE.out.bai           // channel: [ val(meta), bai ]
-    json     = PARAPHASE.out.json          // channel: [ val(meta), json ]
-    vcf      = TABIX_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), gz, tbi ]
-
+    bam      = PARAPHASE.out.bam           // channel: [ val(meta), path(bam) ]
+    bai      = PARAPHASE.out.bai           // channel: [ val(meta), path(bai) ]
+    json     = PARAPHASE.out.json          // channel: [ val(meta), path(json) ]
+    vcf      = PARAPHASE.out.vcf           // channel: [ val(meta), path(vcfs) ]
+    tbi      = PARAPHASE.out.vcf_index     // channel: [ val(meta), path(tbis) ]
     versions = ch_versions                 // channel: [ versions.yml ]
 }
 
diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf
index 8b71453e..8a1ddbea 100644
--- a/subworkflows/local/call_repeat_expansions/main.nf
+++ b/subworkflows/local/call_repeat_expansions/main.nf
@@ -1,9 +1,10 @@
-include { TRGT                                   } from '../../../modules/local/trgt'
+include { ADD_FOUND_IN_TAG                       } from '../../../modules/local/add_found_in_tag/main'
+include { TRGT_GENOTYPE                          } from '../../../modules/nf-core/trgt/genotype/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_TRGT  } from '../../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_SORT as SAMTOOLS_SORT_TRGT    } from '../../../modules/nf-core/samtools/sort/main'
 include { BCFTOOLS_SORT as BCFTOOLS_SORT_TRGT    } from '../../../modules/nf-core/bcftools/sort/main'
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_MERGE } from '../../../modules/nf-core/bcftools/index/main'
-include { BCFTOOLS_MERGE                         } from '../../../modules/nf-core/bcftools/merge/main'
+include { TRGT_MERGE                             } from '../../../modules/nf-core/trgt/merge/main'
+include { BCFTOOLS_INDEX                         } from '../../../modules/nf-core/bcftools/index/main'
 
 workflow CALL_REPEAT_EXPANSIONS {
 
@@ -18,38 +19,64 @@ workflow CALL_REPEAT_EXPANSIONS {
     ch_versions         = Channel.empty()
 
     ch_bam_bai
-        .map { meta, bam, bai -> [meta, bam, bai, meta.sex] }
+        .map { meta, bam, bai -> [ meta, bam, bai, meta.sex == 1 ? 'XY' : 'XX' ] }
         .set { ch_trgt_input }
 
     // Run TGRT
-    TRGT ( ch_trgt_input, ch_fasta, ch_fai, ch_trgt_bed.map { it[1] } )
+    TRGT_GENOTYPE (
+        ch_trgt_input,
+        ch_fasta,
+        ch_fai,
+        ch_trgt_bed
+    )
+    ch_versions = ch_versions.mix(TRGT_GENOTYPE.out.versions)
 
     // Sort and index bam
-    SAMTOOLS_SORT_TRGT ( TRGT.out.bam, [[],[]] )
-    SAMTOOLS_INDEX_TRGT(SAMTOOLS_SORT_TRGT.out.bam)
+    SAMTOOLS_SORT_TRGT (
+        TRGT_GENOTYPE.out.bam,
+        [[],[]]
+    )
+    ch_versions = ch_versions.mix(SAMTOOLS_SORT_TRGT.out.versions)
+
+    SAMTOOLS_INDEX_TRGT ( SAMTOOLS_SORT_TRGT.out.bam )
+    ch_versions = ch_versions.mix(SAMTOOLS_INDEX_TRGT.out.versions)
+
+    // Add FOUND_IN=TRGT tag
+    ADD_FOUND_IN_TAG (
+        TRGT_GENOTYPE.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        "TRGT"
+    )
 
     // Sort and index bcf
-    BCFTOOLS_SORT_TRGT(TRGT.out.vcf)
+    BCFTOOLS_SORT_TRGT ( ADD_FOUND_IN_TAG.out.vcf )
+    ch_versions = ch_versions.mix(BCFTOOLS_SORT_TRGT.out.versions)
 
     BCFTOOLS_SORT_TRGT.out.vcf
         .join( BCFTOOLS_SORT_TRGT.out.tbi )
-        .map { meta, bcf, csi -> [ [ id : meta.project ], bcf, csi ] }
+        .map { meta, bcf, csi -> [ [ id : meta.family_id ], bcf, csi ] }
         .groupTuple()
-        .set{ ch_bcftools_merge_in }
+        .set{ ch_trgt_merge_in }
 
-    BCFTOOLS_MERGE ( ch_bcftools_merge_in, ch_fasta, ch_fai, [] )
+    TRGT_MERGE (
+        ch_trgt_merge_in,
+        [[],[]],
+        [[],[]],
+    )
+    ch_versions = ch_versions.mix(TRGT_MERGE.out.versions)
 
-    BCFTOOLS_INDEX_MERGE ( BCFTOOLS_MERGE.out.merged_variants )
+    BCFTOOLS_INDEX(
+        TRGT_MERGE.out.vcf
+    )
+    ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions)
 
-    ch_versions = ch_versions.mix(TRGT.out.versions)
-    ch_versions = ch_versions.mix(SAMTOOLS_SORT_TRGT.out.versions)
-    ch_versions = ch_versions.mix(SAMTOOLS_INDEX_TRGT.out.versions)
-    ch_versions = ch_versions.mix(BCFTOOLS_SORT_TRGT.out.versions)
-    ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions)
-    ch_versions = ch_versions.mix(BCFTOOLS_INDEX_MERGE.out.versions)
 
     emit:
-    vcf      = BCFTOOLS_SORT_TRGT.out.vcf  // channel: [ val(meta), path(vcf) ]
-    versions = ch_versions                 // channel: [ versions.yml ]
+    sample_vcf  = BCFTOOLS_SORT_TRGT.out.vcf  // channel: [ val(meta), path(vcf) ]
+    sample_tbi  = BCFTOOLS_SORT_TRGT.out.tbi  // channel: [ val(meta), path(tbi) ]
+    family_vcf  = TRGT_MERGE.out.vcf          // channel: [ val(meta), path(vcf) ]
+    family_tbi  = BCFTOOLS_INDEX.out.tbi      // channel: [ val(meta), path(tbi) ]
+    sample_bam  = SAMTOOLS_SORT_TRGT.out.bam  // channel: [ val(meta), path(bam) ]
+    sample_bai  = SAMTOOLS_INDEX_TRGT.out.bai // channel: [ val(meta), path(bai) ]
+    versions    = ch_versions                 // channel: [ versions.yml ]
 }
 
diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test
new file mode 100644
index 00000000..6a5af047
--- /dev/null
+++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test
@@ -0,0 +1,99 @@
+nextflow_workflow {
+
+    name "Test Workflow CALL_REPEAT_EXPANSIONS"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "CALL_REPEAT_EXPANSIONS"
+
+    setup {
+            run("GUNZIP") {
+                script "../../../../modules/nf-core/gunzip/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ],
+                        file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                    ]
+                    """
+                }
+
+            }
+
+            run("SAMTOOLS_FAIDX") {
+                script "../../../../modules/nf-core/samtools/faidx/main.nf"
+                process {
+                    """
+                    input[0] = GUNZIP.out.gunzip
+                    input[1] = [[],[]]
+                    """
+                }
+
+            }
+    }
+
+    test("[bam, bai], fasta, fai, bed") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family', sex: 1 ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of([
+                    [ id: 'pathogenic_repeats' ],
+                    file(params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed')
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_bai.get(0).get(1).endsWith(".bai") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    bam(workflow.out.sample_bam.get(0).get(1), stringency: 'silent').getReadsMD5(),
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("[bam, bai], fasta, fai, bed - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family', sex: 1 ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of([
+                    [ id: 'pathogenic_repeats' ],
+                    file(params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed')
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap
new file mode 100644
index 00000000..84f6ef94
--- /dev/null
+++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap
@@ -0,0 +1,169 @@
+{
+    "[bam, bai], fasta, fai, bed": {
+        "content": [
+            "d7d518f68789d3d51a26be28a93b9654",
+            "51174ac303f7b78f4672f90c13363412",
+            "a51f00198c7449fd64772fe680c6241",
+            [
+                "versions.yml:md5,21f644fc2bb29eb5ed97231b3b95d5d1",
+                "versions.yml:md5,445b9cde08bfee6fc492aec41ccd39c2",
+                "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070",
+                "versions.yml:md5,539d877809cffefa48dd1f20b1381cff",
+                "versions.yml:md5,78d86f9ddc871705ca029444a498322f",
+                "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-09T15:52:26.560152049"
+    },
+    "[bam, bai], fasta, fai, bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,21f644fc2bb29eb5ed97231b3b95d5d1",
+                    "versions.yml:md5,445b9cde08bfee6fc492aec41ccd39c2",
+                    "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070",
+                    "versions.yml:md5,539d877809cffefa48dd1f20b1381cff",
+                    "versions.yml:md5,78d86f9ddc871705ca029444a498322f",
+                    "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family",
+                            "sex": 1
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,21f644fc2bb29eb5ed97231b3b95d5d1",
+                    "versions.yml:md5,445b9cde08bfee6fc492aec41ccd39c2",
+                    "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070",
+                    "versions.yml:md5,539d877809cffefa48dd1f20b1381cff",
+                    "versions.yml:md5,78d86f9ddc871705ca029444a498322f",
+                    "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-09T15:52:40.512924071"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/call_repeat_expansions/tests/nextflow.config b/subworkflows/local/call_repeat_expansions/tests/nextflow.config
new file mode 100644
index 00000000..b51f0527
--- /dev/null
+++ b/subworkflows/local/call_repeat_expansions/tests/nextflow.config
@@ -0,0 +1,14 @@
+process {
+    withName: 'CALL_REPEAT_EXPANSIONS:TRGT_MERGE' {
+        ext.args = '--output-type z --force-single --no-version'
+    }
+    withName: 'CALL_REPEAT_EXPANSIONS:BCFTOOLS_SORT_TRGT' {
+        ext.args = '--output-type z --write-index=tbi'
+    }
+    withName: 'CALL_REPEAT_EXPANSIONS:TRGT' {
+        ext.args = { "--sample-name ${meta.id}" }
+    }
+    withName: 'CALL_REPEAT_EXPANSIONS:BCFTOOLS_INDEX' {
+        ext.args = "--tbi"
+    }
+}
diff --git a/subworkflows/local/call_svs/main.nf b/subworkflows/local/call_svs/main.nf
new file mode 100644
index 00000000..e9bfe5f3
--- /dev/null
+++ b/subworkflows/local/call_svs/main.nf
@@ -0,0 +1,103 @@
+include { ADD_FOUND_IN_TAG                } from '../../../modules/local/add_found_in_tag/main'
+include { SVDB_MERGE                      } from '../../../modules/nf-core/svdb/merge/main'
+include { BCFTOOLS_QUERY                  } from '../../../modules/nf-core/bcftools/query/main'
+include { BCFTOOLS_REHEADER               } from '../../../modules/nf-core/bcftools/reheader/main'
+include { CREATE_SAMPLES_FILE             } from '../../../modules/local/create_samples_file/main'
+include { SEVERUS                         } from '../../../modules/nf-core/severus/main'
+include { SNIFFLES                        } from '../../../modules/nf-core/sniffles/main'
+include { TABIX_TABIX as TABIX_SVDB_MERGE } from '../../../modules/nf-core/tabix/tabix/main'
+
+workflow CALL_SVS {
+
+    take:
+    ch_bam_bai        // channel [mandatory]: [ val(meta), path(bam), path(bai) ]
+    ch_fasta          // channel [mandatory]: [ val(meta), path(fasta) ]
+    ch_fai            // channel [mandatory]: [ val(meta), path(fai) ]
+    sv_caller         //     val [mandatory]: Which caller to use
+    ch_tandem_repeats // channel  [optional]: [ val(meta), path(bed) ]
+    ch_bed            // channel  [optional]: [ val(meta), path(bed) ]
+
+    main:
+    ch_versions     = Channel.empty()
+
+    // Call SVs
+    if (sv_caller == "severus") {
+
+        SEVERUS (
+            ch_bam_bai.map { meta, bam, bai -> [ meta, bam, bai, [], [], [] ] },
+            ch_tandem_repeats
+        )
+        ch_versions = ch_versions.mix(SEVERUS.out.versions)
+
+        SEVERUS.out.all_vcf
+            .set { ch_vcf }
+
+    } else if (sv_caller == "sniffles") {
+
+        SNIFFLES (
+            ch_bam_bai,
+            ch_fasta,
+            ch_tandem_repeats,
+            true,
+            false
+        )
+        ch_versions = ch_versions.mix(SNIFFLES.out.versions)
+
+        SNIFFLES.out.vcf
+            .set { ch_vcf }
+    }
+
+    // Annotate with FOUND_IN tag
+    ADD_FOUND_IN_TAG (
+        ch_vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        sv_caller
+    )
+    ch_versions = ch_versions.mix(ADD_FOUND_IN_TAG.out.versions)
+
+    // Get the sample name from the VCF
+    // For Sniffles this is hardcoded as SAMPLE and for Severus it's based on the filename
+    BCFTOOLS_QUERY (
+        ADD_FOUND_IN_TAG.out.vcf.join(ADD_FOUND_IN_TAG.out.csi),
+        [],
+        [],
+        []
+    )
+    ch_versions = ch_versions.mix(BCFTOOLS_QUERY.out.versions)
+
+    // Creates a "vcf_sample_name meta.id" file for bcftools reheader
+    CREATE_SAMPLES_FILE ( BCFTOOLS_QUERY.out.output )
+    ch_versions = ch_versions.mix(CREATE_SAMPLES_FILE.out.versions)
+
+    ADD_FOUND_IN_TAG.out.vcf
+        .join( CREATE_SAMPLES_FILE.out.samples )
+        .map { meta, vcf, samples -> [ meta, vcf, [], samples ] }
+        .set { ch_bcftools_reheader_in }
+
+    // Give meta.id as sample name in the VCF
+    BCFTOOLS_REHEADER ( ch_bcftools_reheader_in, [[],[]] )
+    ch_versions = ch_versions.mix(BCFTOOLS_REHEADER.out.versions)
+
+    BCFTOOLS_REHEADER.out.vcf
+        .map { meta, vcf -> [ [ 'id': meta.family_id ], vcf ] }
+        .groupTuple()
+        .set { ch_svdb_merge_in }
+
+    // Merge the files with new sample names
+    SVDB_MERGE (
+        ch_svdb_merge_in,
+        [],
+        true
+    )
+    ch_versions = ch_versions.mix(SVDB_MERGE.out.versions)
+
+    TABIX_SVDB_MERGE ( SVDB_MERGE.out.vcf )
+    ch_versions = ch_versions.mix(TABIX_SVDB_MERGE.out.versions)
+
+    emit:
+    sample_vcf     = BCFTOOLS_REHEADER.out.vcf   // channel: [ val(meta), path(vcf) ]
+    sample_tbi     = BCFTOOLS_REHEADER.out.index // channel: [ val(meta), path(tbi) ]
+    family_vcf  = SVDB_MERGE.out.vcf          // channel: [ val(meta), path(vcf) ]
+    family_tbi  = TABIX_SVDB_MERGE.out.tbi    // channel: [ val(meta), path(tbi) ]
+    versions            = ch_versions                 // channel: [ path(versions.yml) ]
+}
+
diff --git a/subworkflows/local/call_svs/tests/main.nf.test b/subworkflows/local/call_svs/tests/main.nf.test
new file mode 100644
index 00000000..3859de5b
--- /dev/null
+++ b/subworkflows/local/call_svs/tests/main.nf.test
@@ -0,0 +1,624 @@
+nextflow_workflow {
+
+    name "Test Workflow CALL_SVS"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "CALL_SVS"
+
+    setup {
+            run("GUNZIP") {
+                script "../../../../modules/nf-core/gunzip/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ],
+                        file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                    ]
+                    """
+                }
+
+            }
+
+            run("SAMTOOLS_FAIDX") {
+                script "../../../../modules/nf-core/samtools/faidx/main.nf"
+                process {
+                    """
+                    input[0] = GUNZIP.out.gunzip
+                    input[1] = [[],[]]
+                    """
+                }
+
+            }
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], [] - sniffles") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, bed, [] - sniffles") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [
+                    [ id:'trf' ],
+                    file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
+                ]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("2 samples - [bam, bai], fasta, fai, [], [] - sniffles") {
+        tag "x"
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test_1', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                    ],
+                    [
+                        [ id:'test_2', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam.bai', checkIfExists: true)
+                    ]
+                )
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.sample_tbi.get(1).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.sample_vcf.get(1).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(1).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).linesGzip,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], bed - sniffles") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+            input[5] = Channel.of('chr20\t2650000\t2660000')
+                .collectFile(name: 'chr20.bed', newLine: true)
+                .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], [] - severus") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, bed, [] - severus") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [
+                    [ id:'trf' ],
+                    file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
+                ]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], bed - severus") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = Channel.of('chr20\t2650000\t2660000')
+                    .collectFile(name: 'chr20.bed', newLine: true)
+                    .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("2 samples - [bam, bai], fasta, fai, [], [] - severus") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test_1', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                    ],
+                    [
+                        [ id:'test_2', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam.bai', checkIfExists: true)
+                    ]
+                )
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.sample_tbi.get(0).get(1).endsWith("tbi") },
+                { assert workflow.out.sample_tbi.get(1).get(1).endsWith("tbi") },
+                { assert workflow.out.family_tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.sample_vcf.get(1).get(1)).vcf.summary,
+                    path(workflow.out.sample_vcf.get(1).get(1)).vcf.variantsMD5,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.summary,
+                    path(workflow.out.family_vcf.get(0).get(1)).vcf.variantsMD5,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], [] - sniffles -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, bed, [] - sniffles -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [
+                    [ id:'trf' ],
+                    file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
+                ]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], bed - sniffles -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+                input[5] = Channel.of('chr20\t2650000\t2660000')
+                    .collectFile(name: 'chr20.bed', newLine: true)
+                    .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("2 samples - [bam, bai], fasta, fai, [], [] - sniffles -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test_1', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                    ],
+                    [
+                        [ id:'test_2', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam.bai', checkIfExists: true)
+                    ]
+                )
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "sniffles"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.sample_vcf.collect { file(it[1]).name }.sort().toString(), // don't know the order of the output VCFs
+                    workflow.out.sample_tbi,
+                    workflow.out.family_vcf,
+                    workflow.out.family_tbi,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], [] - severus -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, [], bed - severus -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = Channel.of('chr20\t2650000\t2660000')
+                    .collectFile(name: 'chr20.bed', newLine: true)
+                    .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("1 sample - [bam, bai], fasta, fai, bed, [] - severus -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false, family_id: 'family' ], // meta map
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                ])
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [
+                    [ id:'trf' ],
+                    file('https://github.com/fritzsedlazeck/Sniffles/raw/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed', checkIfExists: true)
+                ]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+
+    }
+
+    test("2 samples - [bam, bai], fasta, fai, [], [] - severus -stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test_1', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true)
+                    ],
+                    [
+                        [ id:'test_2', single_end:false, family_id: 'family' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam', checkIfExists: true),
+                        file(params.pipelines_testdata_base_path + 'testdata/HG002_ONT.bam.bai', checkIfExists: true)
+                    ]
+                )
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = "severus"
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.sample_vcf.collect { file(it[1]).name }.sort().toString(), // don't know the order of the output VCFs
+                    workflow.out.sample_tbi,
+                    workflow.out.family_vcf,
+                    workflow.out.family_tbi,
+                    workflow.out.versions,
+                ).match() }
+            )
+        }
+
+    }
+}
diff --git a/subworkflows/local/call_svs/tests/main.nf.test.snap b/subworkflows/local/call_svs/tests/main.nf.test.snap
new file mode 100644
index 00000000..72aa70d4
--- /dev/null
+++ b/subworkflows/local/call_svs/tests/main.nf.test.snap
@@ -0,0 +1,1300 @@
+{
+    "1 sample - [bam, bai], fasta, fai, bed, [] - sniffles -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:29:03.235235925"
+    },
+    "2 samples - [bam, bai], fasta, fai, [], [] - sniffles -stub": {
+        "content": [
+            "[test_1_reheader.vcf.gz, test_2_reheader.vcf.gz]",
+            [
+                [
+                    {
+                        "id": "test_1",
+                        "single_end": false,
+                        "family_id": "family"
+                    },
+                    "test_1_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                [
+                    {
+                        "id": "test_2",
+                        "single_end": false,
+                        "family_id": "family"
+                    },
+                    "test_2_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "family"
+                    },
+                    "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "family"
+                    },
+                    "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:29:33.316947597"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], [] - sniffles -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:28:47.871974459"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], [] - severus": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=56, phased=false, phasedAutodetect=false]",
+            "1294e2ab468789a0bd56e8bcaf578a4",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]",
+            "9788302ce089a9d1896f02355474b721",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
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+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
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+    },
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+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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+                            "family_id": "family"
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+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
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+                "sample_vcf": [
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+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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+            "nextflow": "24.04.4"
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+    },
+    "1 sample - [bam, bai], fasta, fai, [], bed - severus": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=56, phased=false, phasedAutodetect=false]",
+            "1294e2ab468789a0bd56e8bcaf578a4",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]",
+            "9788302ce089a9d1896f02355474b721",
+            [
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+    },
+    "2 samples - [bam, bai], fasta, fai, [], [] - sniffles": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=95, phased=false, phasedAutodetect=false]",
+            "7cd0730159250c8945e2007da414651e",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=120, phased=false, phasedAutodetect=false]",
+            "1a02c1b0c86e5531279218fb39ef62b2",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=2, variantCount=130, phased=false, phasedAutodetect=false]",
+            "7d122c197ef319c573592e5f9356a4c0",
+            [
+                "##fileformat=VCFv4.1",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##source=MergeVCF",
+                "##SVDB_version=2.8.2 cmd=\"/usr/local/bin/svdb --merge --bnd_distance 1000 --overlap .5 --vcf test_1_reheader.vcf.gz test_2_reheader.vcf.gz\"",
+                "##ALT=<ID=BND,Description=\"Breakend; Translocation\">",
+                "##ALT=<ID=DEL,Description=\"Deletion\">",
+                "##ALT=<ID=DUP,Description=\"Duplication\">",
+                "##ALT=<ID=INS,Description=\"Insertion\">",
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+                "##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description=\"Number of reads that support the generated insertion (INS) consensus sequence\">",
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+                "##INFO=<ID=FOUND_IN,Number=1,Type=String,Description=\"Program that called the variant\">",
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+                "##INFO=<ID=NM,Number=.,Type=Float,Description=\"Mean number of query alignment length adjusted mismatches of supporting reads\">",
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+                "##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description=\"Number of reads supporting an INS/DEL SV (non-split events only)\">",
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+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variation\">",
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+                "##contig=<ID=chrUn_KI270393v1,length=1308>",
+                "##contig=<ID=chrUn_KI270384v1,length=1658>",
+                "##contig=<ID=chrUn_KI270392v1,length=971>",
+                "##contig=<ID=chrUn_KI270381v1,length=1930>",
+                "##contig=<ID=chrUn_KI270385v1,length=990>",
+                "##contig=<ID=chrUn_KI270382v1,length=4215>",
+                "##contig=<ID=chrUn_KI270376v1,length=1136>",
+                "##contig=<ID=chrUn_KI270374v1,length=2656>",
+                "##contig=<ID=chrUn_KI270372v1,length=1650>",
+                "##contig=<ID=chrUn_KI270373v1,length=1451>",
+                "##contig=<ID=chrUn_KI270375v1,length=2378>",
+                "##contig=<ID=chrUn_KI270371v1,length=2805>",
+                "##contig=<ID=chrUn_KI270448v1,length=7992>",
+                "##contig=<ID=chrUn_KI270521v1,length=7642>",
+                "##contig=<ID=chrUn_GL000195v1,length=182896>",
+                "##contig=<ID=chrUn_GL000219v1,length=179198>",
+                "##contig=<ID=chrUn_GL000220v1,length=161802>",
+                "##contig=<ID=chrUn_GL000224v1,length=179693>",
+                "##contig=<ID=chrUn_KI270741v1,length=157432>",
+                "##contig=<ID=chrUn_GL000226v1,length=15008>",
+                "##contig=<ID=chrUn_GL000213v1,length=164239>",
+                "##contig=<ID=chrUn_KI270743v1,length=210658>",
+                "##contig=<ID=chrUn_KI270744v1,length=168472>",
+                "##contig=<ID=chrUn_KI270745v1,length=41891>",
+                "##contig=<ID=chrUn_KI270746v1,length=66486>",
+                "##contig=<ID=chrUn_KI270747v1,length=198735>",
+                "##contig=<ID=chrUn_KI270748v1,length=93321>",
+                "##contig=<ID=chrUn_KI270749v1,length=158759>",
+                "##contig=<ID=chrUn_KI270750v1,length=148850>",
+                "##contig=<ID=chrUn_KI270751v1,length=150742>",
+                "##contig=<ID=chrUn_KI270752v1,length=27745>",
+                "##contig=<ID=chrUn_KI270753v1,length=62944>",
+                "##contig=<ID=chrUn_KI270754v1,length=40191>",
+                "##contig=<ID=chrUn_KI270755v1,length=36723>",
+                "##contig=<ID=chrUn_KI270756v1,length=79590>",
+                "##contig=<ID=chrUn_KI270757v1,length=71251>",
+                "##contig=<ID=chrUn_GL000214v1,length=137718>",
+                "##contig=<ID=chrUn_KI270742v1,length=186739>",
+                "##contig=<ID=chrUn_GL000216v2,length=176608>",
+                "##contig=<ID=chrUn_GL000218v1,length=161147>",
+                "##contig=<ID=chrEBV,length=171823>",
+                "##FILTER=<ID=COV_CHANGE,Description=\"Coverage change filter\">",
+                "##FILTER=<ID=COV_MIN,Description=\"Minimum coverage filter\">",
+                "##FILTER=<ID=GT,Description=\"Genotype filter\">",
+                "##FILTER=<ID=NM,Description=\"Alignment noise level filter\">",
+                "##FILTER=<ID=STDEV_LEN,Description=\"SV length standard deviation filter\">",
+                "##FILTER=<ID=STDEV_POS,Description=\"SV Breakpoint standard deviation filter\">",
+                "##FILTER=<ID=STRAND,Description=\"Strand support filter\">",
+                "##FILTER=<ID=SUPPORT_MIN,Description=\"Minimum read support filter\">",
+                "##FILTER=<ID=SVLEN_MIN,Description=\"SV length filter\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=ID,Number=1,Type=String,Description=\"Individual sample SV ID for multi-sample output\">",
+                "##command=\"/usr/local/bin/sniffles --input HG002_PacBio_Revio.bam --reference hg38.test.fa -t 4 --vcf test_1.vcf.gz\"",
+                "##INFO=<ID=VARID,Number=1,Type=String,Description=\"The variant ID of merged samples\">",
+                "##INFO=<ID=FOUNDBY,Number=1,Type=Integer,Description=\"The number of files containing the variant\">",
+                "##INFO=<ID=set,Number=1,Type=String,Description=\"Source VCF for the merged record in SVDB\">",
+                "##INFO=<ID=svdb_origin,Number=1,Type=String,Description=\"pipe separated list of the VCF for the merged record in SVDB\">",
+                "##svdbcmdline=/usr/local/bin/svdb --merge --bnd_distance 1000 --overlap .5 --vcf test_1_reheader.vcf.gz test_2_reheader.vcf.gz",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest_1\ttest_2",
+                "chr16\t81884\tSniffles2.INS.4SF\tN\tCTCCAGGAAGCCCTCCTGAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTATCTCCGGAAGCCCTCCTGAATGCTCCCCACGCTGGCCCCTTCTTCCCACCACCCTACCTCCGGGAAGGCCTCCTGAATGCTCCCCACGCTGGCCCCTTCTTCCCACCACCCTACCTCCGGGAAGCCCTCCTGAATGCTCCCCACGCTGGCCCCTTCTTCCCACCACCCTACCTCCAGGAAGCCCTCCTGAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTATCTCCGGGAAGGCCTCCTGAATGCTCCCCACACTGACCCCTTCTTCCCACCACCCTACCTCCGGGAAGGCCTCCTGAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTAT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=398;END=81884;SUPPORT=12;COVERAGE=22,23,24,23,23;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=68.361;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.INS.4SF|chr16;test_1_reheader_POS=Sniffles2.INS.4SF|81884;test_1_reheader_QUAL=Sniffles2.INS.4SF|60;test_1_reheader_FILTERS=Sniffles2.INS.4SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.4SF|test_1|GT:0/1|GQ:60|DR:12|DV:12;test_1_reheader_INFO=Sniffles2.INS.4SF|IMPRECISE|SVTYPE:INS|SVLEN:398|END:81884|SUPPORT:12|COVERAGE:22:23:24:23:23|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:68.361|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:60:12:12\t./.:.:.:.",
+                "chr16\t81981\tSniffles2.INS.1SF\tN\tCTTGATCACCCTACCTCCGGGAAGGCCTCCTGAATGCTCCCCACGCTGGCCCC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=56;END=81981;SUPPORT=10;COVERAGE=21,21,21,21,23;STRAND=+-;AF=0.476;STDEV_LEN=1.952;STDEV_POS=96.236;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.1SF|chr16;test_2_reheader_POS=Sniffles2.INS.1SF|81981;test_2_reheader_QUAL=Sniffles2.INS.1SF|60;test_2_reheader_FILTERS=Sniffles2.INS.1SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.1SF|test_2|GT:0/1|GQ:60|DR:11|DV:10;test_2_reheader_INFO=Sniffles2.INS.1SF|IMPRECISE|SVTYPE:INS|SVLEN:56|END:81981|SUPPORT:10|COVERAGE:21:21:21:21:23|STRAND:+-|AF:0.476|STDEV_LEN:1.952|STDEV_POS:96.236|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:60:11:10",
+                "chr16\t82055\tSniffles2.INS.3SF\tN\tCTCCGGGAAGCCCTCCTGAATGCTCCCCACGCTGGCCCCTTCTTCCCACCACCCTACCTCCAGGAAGCCCTCCTGAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTATCTCCGGGAAGGCCTCCTCCCTATGCTCCCCACACTGACCCCTTCTTCCCACCACCCTACCTCCGGGAAGGCCTCCTGAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTATCTCCGGGAAGGCCTCCTGAATGCTCCCCACACTGACCCCTTCTTCCCACCACCCTACCTCCGGGAAGGCCTCCTGAGTCACCCGCGCTGACCCCTTCTTCCCACCACCCTATCTCCGGGAAGCCCTCCTAATGCTCCCCGCGCTGACCCCTTCTTCCCACCACCCTAT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=391;END=82055;SUPPORT=7;COVERAGE=20,21,21,22,23;STRAND=+-;AF=0.333;STDEV_LEN=4.147;STDEV_POS=104.55;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.3SF|chr16;test_2_reheader_POS=Sniffles2.INS.3SF|82055;test_2_reheader_QUAL=Sniffles2.INS.3SF|60;test_2_reheader_FILTERS=Sniffles2.INS.3SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.3SF|test_2|GT:0/1|GQ:30|DR:14|DV:7;test_2_reheader_INFO=Sniffles2.INS.3SF|IMPRECISE|SVTYPE:INS|SVLEN:391|END:82055|SUPPORT:7|COVERAGE:20:21:21:22:23|STRAND:+-|AF:0.333|STDEV_LEN:4.147|STDEV_POS:104.55|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:30:14:7",
+                "chr16\t82169\tSniffles2.INS.1SF:test_1_reheader|Sniffles2.INS.2SF:test_2_reheader\tN\tCTCCGGGAAGGCCTCCTGAATGCTCCCCACACTGACCCCTTCTTCCCACCACCCTAC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=57;END=82169;SUPPORT=8;COVERAGE=23,23,23,23,23;STRAND=+-;AF=0.348;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.2SF:test_2_reheader;set=test_1_reheader-filterIntest_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.2SF|chr16;test_1_reheader_POS=Sniffles2.INS.1SF|82169;test_2_reheader_POS=Sniffles2.INS.2SF|82180;test_1_reheader_QUAL=Sniffles2.INS.1SF|60;test_2_reheader_QUAL=Sniffles2.INS.2SF|60;test_1_reheader_FILTERS=Sniffles2.INS.1SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.2SF|GT;test_1_reheader_SAMPLE=Sniffles2.INS.1SF|test_1|GT:0/1|GQ:38|DR:15|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.2SF|test_2|GT:0/0|GQ:22|DR:19|DV:3;test_1_reheader_INFO=Sniffles2.INS.1SF|PRECISE|SVTYPE:INS|SVLEN:57|END:82169|SUPPORT:8|COVERAGE:23:23:23:23:23|STRAND:+-|AF:0.348|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.2SF|IMPRECISE|SVTYPE:INS|SVLEN:111|END:82180|SUPPORT:3|COVERAGE:20:21:22:23:23|STRAND:+-|AF:0.136|STDEV_LEN:3.055|STDEV_POS:113.212|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:38:15:8\t0/0:22:19:3",
+                "chr16\t153120\tSniffles2.INS.5SF:test_1_reheader|Sniffles2.INS.6SF:test_2_reheader\tN\tACAGTGGGGAGGGGACAGTGGGGAGAGGACAGTAAGGAGGGGACCATGGGGAGGAC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=56;END=153120;SUPPORT=23;COVERAGE=22,23,23,23,23;STRAND=+-;AF=1;STDEV_LEN=0.48;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.6SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.5SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.6SF|chr16;test_1_reheader_POS=Sniffles2.INS.5SF|153120;test_2_reheader_POS=Sniffles2.INS.6SF|153120;test_1_reheader_QUAL=Sniffles2.INS.5SF|60;test_2_reheader_QUAL=Sniffles2.INS.6SF|60;test_1_reheader_FILTERS=Sniffles2.INS.5SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.6SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.5SF|test_1|GT:1/1|GQ:60|DR:0|DV:23;test_2_reheader_SAMPLE=Sniffles2.INS.6SF|test_2|GT:1/1|GQ:26|DR:1|DV:13;test_1_reheader_INFO=Sniffles2.INS.5SF|PRECISE|SVTYPE:INS|SVLEN:56|END:153120|SUPPORT:23|COVERAGE:22:23:23:23:23|STRAND:+-|AF:1|STDEV_LEN:0.48|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.6SF|PRECISE|SVTYPE:INS|SVLEN:56|END:153120|SUPPORT:13|COVERAGE:14:14:14:14:14|STRAND:+-|AF:0.929|STDEV_LEN:0.916|STDEV_POS:1.061|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:60:0:23\t1/1:26:1:13",
+                "chr16\t160071\tSniffles2.INS.CSF:test_1_reheader|Sniffles2.INS.CSF:test_2_reheader\tN\tGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGAACAGGCTGTGAGGGTGCCCGGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=583;END=160071;SUPPORT=24;COVERAGE=28,28,28,30,27;STRAND=+-;AF=0.857;STDEV_LEN=0.953;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.CSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.CSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.CSF|chr16;test_1_reheader_POS=Sniffles2.INS.CSF|160071;test_2_reheader_POS=Sniffles2.INS.CSF|160091;test_1_reheader_QUAL=Sniffles2.INS.CSF|60;test_2_reheader_QUAL=Sniffles2.INS.CSF|60;test_1_reheader_FILTERS=Sniffles2.INS.CSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.CSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.CSF|test_1|GT:1/1|GQ:26|DR:4|DV:24;test_2_reheader_SAMPLE=Sniffles2.INS.CSF|test_2|GT:1/1|GQ:1|DR:4|DV:15;test_1_reheader_INFO=Sniffles2.INS.CSF|PRECISE|SVTYPE:INS|SVLEN:583|END:160071|SUPPORT:24|COVERAGE:28:28:28:30:27|STRAND:+-|AF:0.857|STDEV_LEN:0.953|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.CSF|PRECISE|SVTYPE:INS|SVLEN:584|END:160091|SUPPORT:15|COVERAGE:18:19:19:20:20|STRAND:+-|AF:0.789|STDEV_LEN:1.356|STDEV_POS:10.025|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:26:4:24\t1/1:1:4:15",
+                "chr16\t160389\tSniffles2.INS.BSF:test_1_reheader|Sniffles2.INS.BSF:test_2_reheader\tN\tGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=328;END=160389;SUPPORT=25;COVERAGE=28,30,30,29,27;STRAND=+-;AF=0.833;STDEV_LEN=0.277;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.BSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.BSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.BSF|chr16;test_1_reheader_POS=Sniffles2.INS.BSF|160389;test_2_reheader_POS=Sniffles2.INS.BSF|160389;test_1_reheader_QUAL=Sniffles2.INS.BSF|60;test_2_reheader_QUAL=Sniffles2.INS.BSF|60;test_1_reheader_FILTERS=Sniffles2.INS.BSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.BSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.BSF|test_1|GT:1/1|GQ:19|DR:5|DV:25;test_2_reheader_SAMPLE=Sniffles2.INS.BSF|test_2|GT:0/1|GQ:8|DR:5|DV:15;test_1_reheader_INFO=Sniffles2.INS.BSF|PRECISE|SVTYPE:INS|SVLEN:328|END:160389|SUPPORT:25|COVERAGE:28:30:30:29:27|STRAND:+-|AF:0.833|STDEV_LEN:0.277|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.BSF|PRECISE|SVTYPE:INS|SVLEN:328|END:160389|SUPPORT:15|COVERAGE:19:20:20:21:19|STRAND:+-|AF:0.75|STDEV_LEN:0.744|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:19:5:25\t0/1:8:5:15",
+                "chr16\t160753\tSniffles2.INS.ESF:test_1_reheader|Sniffles2.INS.9SF:test_2_reheader\tN\tGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=145;END=160753;SUPPORT=27;COVERAGE=30,28,28,27,27;STRAND=+-;AF=0.964;STDEV_LEN=0.352;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.9SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.ESF|chr16;test_2_reheader_CHROM=Sniffles2.INS.9SF|chr16;test_1_reheader_POS=Sniffles2.INS.ESF|160753;test_2_reheader_POS=Sniffles2.INS.9SF|160753;test_1_reheader_QUAL=Sniffles2.INS.ESF|60;test_2_reheader_QUAL=Sniffles2.INS.9SF|60;test_1_reheader_FILTERS=Sniffles2.INS.ESF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.9SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.ESF|test_1|GT:1/1|GQ:60|DR:1|DV:27;test_2_reheader_SAMPLE=Sniffles2.INS.9SF|test_2|GT:1/1|GQ:27|DR:2|DV:17;test_1_reheader_INFO=Sniffles2.INS.ESF|PRECISE|SVTYPE:INS|SVLEN:145|END:160753|SUPPORT:27|COVERAGE:30:28:28:27:27|STRAND:+-|AF:0.964|STDEV_LEN:0.352|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.9SF|PRECISE|SVTYPE:INS|SVLEN:145|END:160753|SUPPORT:17|COVERAGE:20:19:19:19:20|STRAND:+-|AF:0.895|STDEV_LEN:1.612|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:60:1:27\t1/1:27:2:17",
+                "chr16\t163320\tSniffles2.DEL.5DSF:test_1_reheader|Sniffles2.DEL.8FSF:test_2_reheader\tagtgagtaggagacagtggggagaggacagtggagaggggacagtgaggaggggaccatgggaaggggaccgtggagtggggacagtgaggaggggaccatagggagggga\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-111;END=163431;SUPPORT=7;COVERAGE=23,22,22,22,22;STRAND=+-;AF=0.318;STDEV_LEN=1.095;STDEV_POS=10.733;FOUND_IN=sniffles;VARID=Sniffles2.DEL.8FSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.5DSF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.8FSF|chr16;test_1_reheader_POS=Sniffles2.DEL.5DSF|163320;test_2_reheader_POS=Sniffles2.DEL.8FSF|163320;test_1_reheader_QUAL=Sniffles2.DEL.5DSF|60;test_2_reheader_QUAL=Sniffles2.DEL.8FSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.5DSF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.8FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.5DSF|test_1|GT:0/1|GQ:28|DR:15|DV:7;test_2_reheader_SAMPLE=Sniffles2.DEL.8FSF|test_2|GT:0/1|GQ:49|DR:11|DV:8;test_1_reheader_INFO=Sniffles2.DEL.5DSF|PRECISE|SVTYPE:DEL|SVLEN:-111|END:163431|SUPPORT:7|COVERAGE:23:22:22:22:22|STRAND:+-|AF:0.318|STDEV_LEN:1.095|STDEV_POS:10.733|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.8FSF|PRECISE|SVTYPE:DEL|SVLEN:-111|END:163431|SUPPORT:8|COVERAGE:19:19:19:19:18|STRAND:+-|AF:0.421|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:28:15:7\t0/1:49:11:8",
+                "chr16\t163591\tSniffles2.DEL.5ESF:test_1_reheader|Sniffles2.DEL.92SF:test_2_reheader\tggaggggaccgtgggaaggagacagtgaggaggggaccttggggaggggacagtgaggaggggaccatggggaggggacagtgaggaggggacaatggagaggggacagtgaggaggggactgtggggagaggacagtgaggaggggaccatggggagggcacagtggggaggggagagtgaggaagggacagtgaggaggggactgtgg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-210;END=163801;SUPPORT=7;COVERAGE=22,22,22,22,21;STRAND=+-;AF=0.318;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.92SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.5ESF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.92SF|chr16;test_1_reheader_POS=Sniffles2.DEL.5ESF|163591;test_2_reheader_POS=Sniffles2.DEL.92SF|163594;test_1_reheader_QUAL=Sniffles2.DEL.5ESF|60;test_2_reheader_QUAL=Sniffles2.DEL.92SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.5ESF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.92SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.5ESF|test_1|GT:0/1|GQ:28|DR:15|DV:7;test_2_reheader_SAMPLE=Sniffles2.DEL.92SF|test_2|GT:0/1|GQ:49|DR:11|DV:8;test_1_reheader_INFO=Sniffles2.DEL.5ESF|PRECISE|SVTYPE:DEL|SVLEN:-210|END:163801|SUPPORT:7|COVERAGE:22:22:22:22:21|STRAND:+-|AF:0.318|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.92SF|PRECISE|SVTYPE:DEL|SVLEN:-209|END:163803|SUPPORT:8|COVERAGE:20:19:19:18:18|STRAND:+-|AF:0.421|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:28:15:7\t0/1:49:11:8",
+                "chr16\t164801\tSniffles2.INS.FSF:test_1_reheader|Sniffles2.INS.ESF:test_2_reheader\tN\tCGGGGTCGCGGGGCGGGCGGGTCGCGGGGCGGGGTCGCGGGGGCGGGCGAGGTC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=54;END=164801;SUPPORT=8;COVERAGE=21,21,21,21,21;STRAND=+-;AF=0.381;STDEV_LEN=2.16;STDEV_POS=17.972;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.ESF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.FSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.ESF|chr16;test_1_reheader_POS=Sniffles2.INS.FSF|164801;test_2_reheader_POS=Sniffles2.INS.ESF|164801;test_1_reheader_QUAL=Sniffles2.INS.FSF|60;test_2_reheader_QUAL=Sniffles2.INS.ESF|60;test_1_reheader_FILTERS=Sniffles2.INS.FSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.ESF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.FSF|test_1|GT:0/1|GQ:43|DR:13|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.ESF|test_2|GT:0/1|GQ:52|DR:10|DV:8;test_1_reheader_INFO=Sniffles2.INS.FSF|PRECISE|SVTYPE:INS|SVLEN:54|END:164801|SUPPORT:8|COVERAGE:21:21:21:21:21|STRAND:+-|AF:0.381|STDEV_LEN:2.16|STDEV_POS:17.972|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.ESF|IMPRECISE|SVTYPE:INS|SVLEN:59|END:164801|SUPPORT:8|COVERAGE:18:18:18:18:17|STRAND:+-|AF:0.444|STDEV_LEN:5.565|STDEV_POS:38.821|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:43:13:8\t0/1:52:10:8",
+                "chr16\t182789\tSniffles2.INS.10SF:test_1_reheader|Sniffles2.INS.FSF:test_2_reheader\tN\tTGAAACACCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATAGTGGCGGGCGCCTGTAATCCCAGCTGTTCGGGAGGCTGAGGCAGGACAATCACTTAAACCAGGGAAGCAGAGGTTGCAGTGAGCTGAGATCGAGCCACTGCACTCCAGCCTGGGCGACAGACCGAGACTGTCTCAAAAAAAAGACCGGGCACGGTGGCTCACGCCTGTAATCCCACCACTTTGGGAGGCTGAGGCGGGCTGATCACGATGTCAGGAGATCTAGACCATCCTGGCCAACATGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=286;END=182789;SUPPORT=12;COVERAGE=13,12,12,12,12;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.FSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.10SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.FSF|chr16;test_1_reheader_POS=Sniffles2.INS.10SF|182789;test_2_reheader_POS=Sniffles2.INS.FSF|182789;test_1_reheader_QUAL=Sniffles2.INS.10SF|60;test_2_reheader_QUAL=Sniffles2.INS.FSF|60;test_1_reheader_FILTERS=Sniffles2.INS.10SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.10SF|test_1|GT:1/1|GQ:33|DR:0|DV:12;test_2_reheader_SAMPLE=Sniffles2.INS.FSF|test_2|GT:1/1|GQ:2|DR:2|DV:8;test_1_reheader_INFO=Sniffles2.INS.10SF|PRECISE|SVTYPE:INS|SVLEN:286|END:182789|SUPPORT:12|COVERAGE:13:12:12:12:12|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.FSF|PRECISE|SVTYPE:INS|SVLEN:286|END:182789|SUPPORT:8|COVERAGE:10:10:10:10:10|STRAND:+-|AF:0.8|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:33:0:12\t1/1:2:2:8",
+                "chr16\t186052\tSniffles2.DEL.5FSF\tggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacgggg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-629;END=186681;SUPPORT=6;COVERAGE=11,11,11,11,11;STRAND=+-;AF=0.545;STDEV_LEN=8.5;STDEV_POS=8.5;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.5FSF|chr16;test_1_reheader_POS=Sniffles2.DEL.5FSF|186052;test_1_reheader_QUAL=Sniffles2.DEL.5FSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.5FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.5FSF|test_1|GT:0/1|GQ:33|DR:5|DV:6;test_1_reheader_INFO=Sniffles2.DEL.5FSF|PRECISE|SVTYPE:DEL|SVLEN:-629|END:186681|SUPPORT:6|COVERAGE:11:11:11:11:11|STRAND:+-|AF:0.545|STDEV_LEN:8.5|STDEV_POS:8.5|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:33:5:6\t./.:.:.:.",
+                "chr16\t186294\tSniffles2.DEL.60SF:test_1_reheader|Sniffles2.DEL.96SF:test_2_reheader\tcagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacggggggaacagcgacacgggg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-863;END=187157;SUPPORT=5;COVERAGE=11,11,11,11,10;STRAND=+-;AF=0.455;STDEV_LEN=0.577;STDEV_POS=6.928;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.DEL.96SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.60SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.96SF|chr16;test_1_reheader_POS=Sniffles2.DEL.60SF|186294;test_2_reheader_POS=Sniffles2.DEL.96SF|186313;test_1_reheader_QUAL=Sniffles2.DEL.60SF|60;test_2_reheader_QUAL=Sniffles2.DEL.96SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.60SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.96SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.60SF|test_1|GT:0/1|GQ:33|DR:6|DV:5;test_2_reheader_SAMPLE=Sniffles2.DEL.96SF|test_2|GT:0/1|GQ:10|DR:3|DV:7;test_1_reheader_INFO=Sniffles2.DEL.60SF|PRECISE|SVTYPE:DEL|SVLEN:-863|END:187157|SUPPORT:5|COVERAGE:11:11:11:11:10|STRAND:+-|AF:0.455|STDEV_LEN:0.577|STDEV_POS:6.928|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.96SF|IMPRECISE|SVTYPE:DEL|SVLEN:-830|END:187143|SUPPORT:7|COVERAGE:10:10:10:10:10|STRAND:+-|AF:0.7|STDEV_LEN:9.815|STDEV_POS:21.245|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:33:6:5\t0/1:10:3:7",
+                "chr16\t239176\tSniffles2.INS.10SF\tN\tTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGGGCTTGCAGTGAGCCGAGATCACGCCACTACACTCGAGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAGCAAACATAATGAAAATTAAAAAATTTTTAAAAAAACCCTGCAAACTTGGTGAATTTTTTACCGACTCGTGCTTTGCAAAATTCTTCATGGAACTTAGATTATATCAGGAAGATGTTAAAAAAAAAAAAAAAAAAAAGAATGCTGACTCCTAACCAAATAACTATGAAGCAGATGCTGAGAGATCAAAGGAGCAAATCTAAAAATCATCAGAGATGGGGCCTGGGGGAGAAGTATGCTGGCTTATAGATGAAAATGACTGGCTCTGTGTTGATAACTGTTGATAACTGTTGGACCTGGGTAATGGGTTTATGAGGCTGGTGTTCTCTACTTTTGTTAATGTTTGAGCATTTACATAATAAAGGTTTTTTTTTTTCATTGTATATAGAAATGGACTCACTATGTTGCCCAGGCTGGCCTCAAATTCCCGGGCTCAAGTAGTCCTCCCTCCTCTGCCTCTTGAAGTGCTGAGATTATAGGCATGAGACACCACACCTGGATCAAAGGTTAAAAAAATAATGATAAAAGAAGTAAGTTGAGGCTACTGTGGGCACACTGCCCATGGGTTAGCCCTGCTGTGCAAGGATCAGAAAAAAAAAAAAAAAAGAAATTGAAGCTAAGGCCTAATTAACTGGCTTATCTTGTAGAGTTTAGCAGAAGTGACCAAGTTTAGAGTTATACTTTATCTTTTTCTTTCTCTGCCCCCTACTTAATGAAGGACAAAAATGAGTAACATGGCTGGGTGTGGTGGCTCACGCCTGTCATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCATGGCCAACATGATGAAACCAAAATACAAAAGTTAGCCAGGCGTGGTGGCGGGCGTA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=1020;END=239176;SUPPORT=2;COVERAGE=2,2,2,2,4;STRAND=+;AF=1;STDEV_LEN=1.414;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.10SF|chr16;test_2_reheader_POS=Sniffles2.INS.10SF|239176;test_2_reheader_QUAL=Sniffles2.INS.10SF|60;test_2_reheader_FILTERS=Sniffles2.INS.10SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.10SF|test_2|GT:1/1|GQ:5|DR:0|DV:2;test_2_reheader_INFO=Sniffles2.INS.10SF|PRECISE|SVTYPE:INS|SVLEN:1020|END:239176|SUPPORT:2|COVERAGE:2:2:2:2:4|STRAND:+|AF:1|STDEV_LEN:1.414|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:5:0:2",
+                "chr16\t318898\tSniffles2.INS.12SF\tN\tGCCAGGGCCTTGGTGAGAGCGGCTCTGACCCCTGGCTGTGCGGAGAGAATGCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=53;END=318898;SUPPORT=4;COVERAGE=12,12,12,12,12;STRAND=+-;AF=0.333;STDEV_LEN=2.082;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.12SF|chr16;test_2_reheader_POS=Sniffles2.INS.12SF|318898;test_2_reheader_QUAL=Sniffles2.INS.12SF|60;test_2_reheader_FILTERS=Sniffles2.INS.12SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.12SF|test_2|GT:0/1|GQ:17|DR:8|DV:4;test_2_reheader_INFO=Sniffles2.INS.12SF|PRECISE|SVTYPE:INS|SVLEN:53|END:318898|SUPPORT:4|COVERAGE:12:12:12:12:12|STRAND:+-|AF:0.333|STDEV_LEN:2.082|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:17:8:4",
+                "chr16\t321645\tSniffles2.INS.13SF\tN\tGGATTCCAACCCACGAAGGGTTAAACCCTCTCATAGCTGGGAATATGAGGTAGAAGGCGGATGCCAACCCACGAAGGGTTAAACCCTCTCATAGCTGGGAATATGAGGTAGAAGGC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=116;END=321645;SUPPORT=8;COVERAGE=16,16,16,15,16;STRAND=+-;AF=0.5;STDEV_LEN=0.548;STDEV_POS=45.616;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.13SF|chr16;test_2_reheader_POS=Sniffles2.INS.13SF|321645;test_2_reheader_QUAL=Sniffles2.INS.13SF|60;test_2_reheader_FILTERS=Sniffles2.INS.13SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.13SF|test_2|GT:0/1|GQ:57|DR:8|DV:8;test_2_reheader_INFO=Sniffles2.INS.13SF|IMPRECISE|SVTYPE:INS|SVLEN:116|END:321645|SUPPORT:8|COVERAGE:16:16:16:15:16|STRAND:+-|AF:0.5|STDEV_LEN:0.548|STDEV_POS:45.616|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:57:8:8",
+                "chr16\t362990\tSniffles2.INS.12SF:test_1_reheader|Sniffles2.INS.14SF:test_2_reheader\tN\tGACTTAGCACCGGGGGGTCTCGGGCTGCGGCTGCTCTCCCA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=42;END=362990;SUPPORT=3;COVERAGE=7,6,6,6,5;STRAND=+-;AF=0.5;STDEV_LEN=0.577;STDEV_POS=9.238;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.14SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.12SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.14SF|chr16;test_1_reheader_POS=Sniffles2.INS.12SF|362990;test_2_reheader_POS=Sniffles2.INS.14SF|362984;test_1_reheader_QUAL=Sniffles2.INS.12SF|60;test_2_reheader_QUAL=Sniffles2.INS.14SF|60;test_1_reheader_FILTERS=Sniffles2.INS.12SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.14SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.12SF|test_1|GT:0/1|GQ:21|DR:3|DV:3;test_2_reheader_SAMPLE=Sniffles2.INS.14SF|test_2|GT:0/1|GQ:46|DR:8|DV:12;test_1_reheader_INFO=Sniffles2.INS.12SF|PRECISE|SVTYPE:INS|SVLEN:42|END:362990|SUPPORT:3|COVERAGE:7:6:6:6:5|STRAND:+-|AF:0.5|STDEV_LEN:0.577|STDEV_POS:9.238|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.14SF|PRECISE|SVTYPE:INS|SVLEN:41|END:362984|SUPPORT:12|COVERAGE:20:20:20:20:19|STRAND:+-|AF:0.6|STDEV_LEN:0.408|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:21:3:3\t0/1:46:8:12",
+                "chr16\t370391\tSniffles2.INS.13SF:test_1_reheader|Sniffles2.INS.16SF:test_2_reheader\tN\tCTACCCTGCCCCGGCTCTCACCCCCTACCCCCGGCCCCCGGCTCTCACCCCCTACCCCGGCCCCGGCTCTCACCCGCTACCCCGGCCCCCGGCTCTCACCCCCTACCCCGGGCCCCCGGCTCTCACCCGCTACCCCGGCCCCGGCTCTCACCCCCTACCCCGGCCCCGGCTCTCACCTCCTACCCCGGCCCCGGCTCTCACCCGCTACCCTGCCCCCGGCTCTCACCGCTACCCCCCGGCTCTCACCCGCTACCCCGCCCCCGGCTCTCACCTCCTACCCCGGCCCCGGCTCTCACCCCCTACCCCGGCCCCCGGCTCTCACCCGCTACCCCCGGCCCCCCGGCTCTCACCTCCTACCCGGCCCCGGCTCTCACCCGCTCCCCCGGCCCCCGGCTCTCACCCGCTCACCCCCGGCCCCCGGCTCTCACCTCCTACCCCGGCCTCGGCTCTCACCCCCTACCCCGGCCCCGGCTCTCACCCCCTACCCCTGCCCCGGCTCTCACCCGCTACCCCGGCCCCCGGCTCTCACCCCCTACCCCGGCCCCCGGCTCTCACCCGCTACCCGGCCCCCGGCTCTCACCTCCTACCCCGGCCCCGGCTCTCACCCGCTACCCCGGCCCCCGGCTCTCACCTCCTACCCCGGCCCGGCTCTCACCCGCTACCCCGGCCCCGGCTCTCACCCCCTACCCCGGCCCCCGGCTCTCACCCGCTACCCCGGCCCCCGGGCTCTCACTCC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=736;END=370391;SUPPORT=7;COVERAGE=7,7,7,7,7;STRAND=+-;AF=1;STDEV_LEN=65.282;STDEV_POS=1.095;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.16SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.13SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.16SF|chr16;test_1_reheader_POS=Sniffles2.INS.13SF|370391;test_2_reheader_POS=Sniffles2.INS.16SF|370391;test_1_reheader_QUAL=Sniffles2.INS.13SF|60;test_2_reheader_QUAL=Sniffles2.INS.16SF|60;test_1_reheader_FILTERS=Sniffles2.INS.13SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.16SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.13SF|test_1|GT:1/1|GQ:19|DR:0|DV:7;test_2_reheader_SAMPLE=Sniffles2.INS.16SF|test_2|GT:1/1|GQ:3|DR:3|DV:12;test_1_reheader_INFO=Sniffles2.INS.13SF|IMPRECISE|SVTYPE:INS|SVLEN:736|END:370391|SUPPORT:7|COVERAGE:7:7:7:7:7|STRAND:+-|AF:1|STDEV_LEN:65.282|STDEV_POS:1.095|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.16SF|IMPRECISE|SVTYPE:INS|SVLEN:648|END:370391|SUPPORT:12|COVERAGE:18:15:15:15:18|STRAND:+-|AF:0.8|STDEV_LEN:59.3|STDEV_POS:1.069|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:19:0:7\t1/1:3:3:12",
+                "chr16\t378308\tSniffles2.INS.14SF:test_1_reheader|Sniffles2.INS.18SF:test_2_reheader\tN\tCCACTCTGACTGCCATCGCCACTCTGACTGCCATCC\t60\tGT\tPRECISE;SVTYPE=INS;SVLEN=36;END=378308;SUPPORT=4;COVERAGE=17,17,17,18,18;STRAND=+-;AF=0.235;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.18SF:test_2_reheader;set=filterIntest_1_reheader-test_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.14SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.18SF|chr16;test_1_reheader_POS=Sniffles2.INS.14SF|378308;test_2_reheader_POS=Sniffles2.INS.18SF|378308;test_1_reheader_QUAL=Sniffles2.INS.14SF|60;test_2_reheader_QUAL=Sniffles2.INS.18SF|60;test_1_reheader_FILTERS=Sniffles2.INS.14SF|GT;test_2_reheader_FILTERS=Sniffles2.INS.18SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.14SF|test_1|GT:0/1|GQ:3|DR:13|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.18SF|test_2|GT:0/1|GQ:52|DR:10|DV:8;test_1_reheader_INFO=Sniffles2.INS.14SF|PRECISE|SVTYPE:INS|SVLEN:36|END:378308|SUPPORT:4|COVERAGE:17:17:17:18:18|STRAND:+-|AF:0.235|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.18SF|PRECISE|SVTYPE:INS|SVLEN:36|END:378308|SUPPORT:8|COVERAGE:19:18:18:18:18|STRAND:+-|AF:0.444|STDEV_LEN:0.447|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:3:13:4\t0/1:52:10:8",
+                "chr16\t378517\tSniffles2.INS.15SF:test_1_reheader|Sniffles2.INS.1ASF:test_2_reheader\tN\tGCCATCGCCACCCGCACTGCCATCGCCACCCGCACTGCCATCGCCACCCTGACTGCCATCGCCACCCACACTGCCATCCCCACCCGCACTGCCATCGCCACCCTGACTGCCATCGCCACCCACAATGCCATCCCCACCCGCACTGCCATCGCCACCCGCACTGCCATCCCCACCCGCACTGCCATCGCCACCCGCACTGCCATCGCCACCCGCACTGCCATCGCCACCCACACTGCCATC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=240;END=378517;SUPPORT=12;COVERAGE=17,18,18,18,18;STRAND=+-;AF=0.667;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.1ASF:test_2_reheader;set=test_1_reheader-filterIntest_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.15SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.1ASF|chr16;test_1_reheader_POS=Sniffles2.INS.15SF|378517;test_2_reheader_POS=Sniffles2.INS.1ASF|378517;test_1_reheader_QUAL=Sniffles2.INS.15SF|60;test_2_reheader_QUAL=Sniffles2.INS.1ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.15SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.1ASF|GT;test_1_reheader_SAMPLE=Sniffles2.INS.15SF|test_1|GT:0/1|GQ:26|DR:6|DV:12;test_2_reheader_SAMPLE=Sniffles2.INS.1ASF|test_2|GT:0/0|GQ:11|DR:15|DV:3;test_1_reheader_INFO=Sniffles2.INS.15SF|PRECISE|SVTYPE:INS|SVLEN:240|END:378517|SUPPORT:12|COVERAGE:17:18:18:18:18|STRAND:+-|AF:0.667|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.1ASF|PRECISE|SVTYPE:INS|SVLEN:240|END:378517|SUPPORT:3|COVERAGE:19:18:18:18:18|STRAND:+-|AF:0.167|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:26:6:12\t0/0:11:15:3",
+                "chr16\t397717\tSniffles2.INS.16SF:test_1_reheader|Sniffles2.INS.1DSF:test_2_reheader\tN\tTGAGGGAGTCGGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGTGGGGGTGGGGGTGTGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGTGGGGGTGAGGGAGTCGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGTGGGGGGTGAGGGAGTCGGGGGGTGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGGGTGAGGGAGTCGGGGGGTGGGGGTGGGGGTGGGGGGGC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=491;END=397717;SUPPORT=3;COVERAGE=3,3,3,3,3;STRAND=+-;AF=1;STDEV_LEN=2.309;STDEV_POS=5.196;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.1DSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.16SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.1DSF|chr16;test_1_reheader_POS=Sniffles2.INS.16SF|397717;test_2_reheader_POS=Sniffles2.INS.1DSF|397727;test_1_reheader_QUAL=Sniffles2.INS.16SF|60;test_2_reheader_QUAL=Sniffles2.INS.1DSF|60;test_1_reheader_FILTERS=Sniffles2.INS.16SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.1DSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.16SF|test_1|GT:1/1|GQ:8|DR:0|DV:3;test_2_reheader_SAMPLE=Sniffles2.INS.1DSF|test_2|GT:0/1|GQ:9|DR:4|DV:11;test_1_reheader_INFO=Sniffles2.INS.16SF|PRECISE|SVTYPE:INS|SVLEN:491|END:397717|SUPPORT:3|COVERAGE:3:3:3:3:3|STRAND:+-|AF:1|STDEV_LEN:2.309|STDEV_POS:5.196|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.1DSF|IMPRECISE|SVTYPE:INS|SVLEN:506|END:397727|SUPPORT:11|COVERAGE:18:15:15:15:16|STRAND:+-|AF:0.733|STDEV_LEN:34.854|STDEV_POS:7.448|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:8:0:3\t0/1:9:4:11",
+                "chr16\t410360\tSniffles2.DEL.99SF\ttcttccgggtgggtgcctcgtgcgctctgtgagaag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-36;END=410396;SUPPORT=7;COVERAGE=15,14,14,14,12;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.99SF|chr16;test_2_reheader_POS=Sniffles2.DEL.99SF|410360;test_2_reheader_QUAL=Sniffles2.DEL.99SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.99SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.99SF|test_2|GT:0/1|GQ:50|DR:7|DV:7;test_2_reheader_INFO=Sniffles2.DEL.99SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:410396|SUPPORT:7|COVERAGE:15:14:14:14:12|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:50:7:7",
+                "chr16\t433138\tSniffles2.INS.21SF\tN\tATTCTCCTGCCTCAGCCTCCCAAGAAGCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTATATTTTTAGTAGAGACGAAGTTTCACCATGTTAGCCAGGATGGTCTCCATCTCCTGACCTCGTGATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCTACTGTGCCCGGCCTGTCATTTTTATATATTGGGAAAGTTTTGAGTCCTTTCTCTAGGTATGTTGAAATATACAGGCATGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGTCCGAGGCGGGTGAATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCCAGGCATGGTGGTGGGCGCCTGTAGTCCCAGCTACTCCAGAGGCTGAGGCAGGAGAATGGCGTGAACCTGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACTGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAGAAATATACAATATATTGTTGTTAAATTTAGTCACCCTACTCTGCTACCAAACATTAGAACTTATCCTTTGTCTCATTGTAATTTTTTTTTTTTTGAGATGGGGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCTATCTTGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=725;END=433138;SUPPORT=2;COVERAGE=4,4,4,4,3;STRAND=+-;AF=0.5;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.21SF|chr16;test_2_reheader_POS=Sniffles2.INS.21SF|433138;test_2_reheader_QUAL=Sniffles2.INS.21SF|60;test_2_reheader_FILTERS=Sniffles2.INS.21SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.21SF|test_2|GT:0/1|GQ:14|DR:2|DV:2;test_2_reheader_INFO=Sniffles2.INS.21SF|PRECISE|SVTYPE:INS|SVLEN:725|END:433138|SUPPORT:2|COVERAGE:4:4:4:4:3|STRAND:+-|AF:0.5|STDEV_LEN:0.707|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:14:2:2",
+                "chr16\t433317\tSniffles2.DEL.9CSF\tcaccgctcattgcatatttctaaccattaaccgtgctctttaccctcctgatgcttcccagcctctgatatcaatcgctctattctctacctccattagatccacttttctagctcccacataagagtaaaaacgtgatatttgtctttctctgcctgtct\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-161;END=433478;SUPPORT=2;COVERAGE=4,4,4,3,3;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.9CSF|chr16;test_2_reheader_POS=Sniffles2.DEL.9CSF|433317;test_2_reheader_QUAL=Sniffles2.DEL.9CSF|60;test_2_reheader_FILTERS=Sniffles2.DEL.9CSF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.9CSF|test_2|GT:0/1|GQ:14|DR:2|DV:2;test_2_reheader_INFO=Sniffles2.DEL.9CSF|PRECISE|SVTYPE:DEL|SVLEN:-161|END:433478|SUPPORT:2|COVERAGE:4:4:4:3:3|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:14:2:2",
+                "chr16\t492363\tSniffles2.INS.22SF\tN\tTCCCGGGGGACCCGAGGCCACCCCGGCCCTCCCGGGAGACCCGAGGCCGCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCGGGAGACCCGAGGCCGCCCCAAGCCCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCGGGAGACCCGCGAGGCCGCCCAGAGCCCTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGTCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCGGGGAGACCCGAGGCCGCCCAGGGCCCTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGGGAGCGATCCCAGGGCCCCTCCCGGGGAGACCCGAGGCCGCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCGGGGAGACCCGAGGCCGCCCAGGGCCCTCCCGGGAGACCCGAGGCCGCCCCAAGCCCTCCCCGGGAGACCCGAGGCCGTCCAGGGCCCTTCCCGGGGAGACCCGAGGCCGCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCGGGGAGACCCGAGGCCGCCCAGGGCCCTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTCCCGGGAGACCCGAGGCCGCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTCCCGGGAGACCCGAGGCCGCCCAGAGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCCAGGGCCCTCCCCGGGAGACCCGAGGCCGCCCAGGGCCC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=1083;END=492363;SUPPORT=2;COVERAGE=2,2,2,2,2;STRAND=+;AF=1;STDEV_LEN=4.243;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.22SF|chr16;test_2_reheader_POS=Sniffles2.INS.22SF|492363;test_2_reheader_QUAL=Sniffles2.INS.22SF|60;test_2_reheader_FILTERS=Sniffles2.INS.22SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.22SF|test_2|GT:1/1|GQ:5|DR:0|DV:2;test_2_reheader_INFO=Sniffles2.INS.22SF|PRECISE|SVTYPE:INS|SVLEN:1083|END:492363|SUPPORT:2|COVERAGE:2:2:2:2:2|STRAND:+|AF:1|STDEV_LEN:4.243|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:5:0:2",
+                "chr16\t494828\tSniffles2.INS.23SF\tN\tGGGAGGTCGAGGCTGCAGAGGTGGCAGGATCACATGATCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGCAGGATCACATGATCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGCAGGATCACATGATCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATAGCATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGATCCTGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGATCCTGGGAGGTCGAGGCTGCTGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGAGGATCACATGAGCCGGGGAGGTCGAGGCTGCAGAGGTGGGGCGGATCACATGAGCCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=2706;END=494828;SUPPORT=2;COVERAGE=2,2,2,2,2;STRAND=+;AF=1;STDEV_LEN=2.121;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.23SF|chr16;test_2_reheader_POS=Sniffles2.INS.23SF|494828;test_2_reheader_QUAL=Sniffles2.INS.23SF|60;test_2_reheader_FILTERS=Sniffles2.INS.23SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.23SF|test_2|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_INFO=Sniffles2.INS.23SF|PRECISE|SVTYPE:INS|SVLEN:2706|END:494828|SUPPORT:2|COVERAGE:2:2:2:2:2|STRAND:+|AF:1|STDEV_LEN:2.121|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:11:0:4",
+                "chr16\t504280\tSniffles2.INS.17SF:test_1_reheader|Sniffles2.INS.24SF:test_2_reheader\tN\tTCCATCTCCTCCTGTACCCCCTCACCTCCTTGTGCACCCCCTCACCTCCTGTACCCCCTCACCTCCTCTGTA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=74;END=504280;SUPPORT=4;COVERAGE=4,4,4,4,4;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.24SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.17SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.24SF|chr16;test_1_reheader_POS=Sniffles2.INS.17SF|504280;test_2_reheader_POS=Sniffles2.INS.24SF|504280;test_1_reheader_QUAL=Sniffles2.INS.17SF|60;test_2_reheader_QUAL=Sniffles2.INS.24SF|60;test_1_reheader_FILTERS=Sniffles2.INS.17SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.24SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.17SF|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.24SF|test_2|GT:0/1|GQ:0|DR:2|DV:7;test_1_reheader_INFO=Sniffles2.INS.17SF|PRECISE|SVTYPE:INS|SVLEN:74|END:504280|SUPPORT:4|COVERAGE:4:4:4:4:4|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.24SF|PRECISE|SVTYPE:INS|SVLEN:74|END:504280|SUPPORT:7|COVERAGE:9:9:9:10:13|STRAND:+-|AF:0.778|STDEV_LEN:0|STDEV_POS:13.416|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t0/1:0:2:7",
+                "chr16\t504419\tSniffles2.INS.18SF:test_1_reheader|Sniffles2.INS.26SF:test_2_reheader\tN\tTCACCTCCTCCTGTACCCCCTCACCTCCTCCTGTACCCCCTCACCTCCTCCTGTACCCCTCACCTCCTTGTGCACCCCCTCACCTCCTGTACCCCCTCACCTCCTCCTGTACCCCCCTCACCTCCTCCTGTACCCCCTCACCTCCTTGTGCACCCCCTCACCTCCTGTACCCCCTCACCTCCTCCTGTACCCCCCTCACCTCCTCCTGTACCCCCTCACCTCCTCCTGTACCCCCTCACCTCCTCCTGTACCCCCT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=256;END=504419;SUPPORT=4;COVERAGE=4,4,4,4,5;STRAND=+-;AF=1;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.26SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.18SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.26SF|chr16;test_1_reheader_POS=Sniffles2.INS.18SF|504419;test_2_reheader_POS=Sniffles2.INS.26SF|504419;test_1_reheader_QUAL=Sniffles2.INS.18SF|60;test_2_reheader_QUAL=Sniffles2.INS.26SF|60;test_1_reheader_FILTERS=Sniffles2.INS.18SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.26SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.18SF|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.26SF|test_2|GT:0/1|GQ:20|DR:4|DV:7;test_1_reheader_INFO=Sniffles2.INS.18SF|PRECISE|SVTYPE:INS|SVLEN:256|END:504419|SUPPORT:4|COVERAGE:4:4:4:4:5|STRAND:+-|AF:1|STDEV_LEN:0.707|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.26SF|PRECISE|SVTYPE:INS|SVLEN:224|END:504419|SUPPORT:7|COVERAGE:9:10:11:11:13|STRAND:+-|AF:0.636|STDEV_LEN:15.566|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t0/1:20:4:7",
+                "chr16\t507740\tSniffles2.INS.28SF\tN\tCGTTTCCCGTTTTCAGTATCATCTGCCCGTTCTGAGCCATTTGCTCTCTAGCCCTACCATACAGCTGTCATCCTAAGGTCC\t60\tGT\tPRECISE;SVTYPE=INS;SVLEN=81;END=507740;SUPPORT=3;COVERAGE=14,14,14,14,16;STRAND=+;AF=0.214;STDEV_LEN=0;STDEV_POS=0.577;SUPPORT_LONG=0;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.28SF|chr16;test_2_reheader_POS=Sniffles2.INS.28SF|507740;test_2_reheader_QUAL=Sniffles2.INS.28SF|60;test_2_reheader_FILTERS=Sniffles2.INS.28SF|GT;test_2_reheader_SAMPLE=Sniffles2.INS.28SF|test_2|GT:0/0|GQ:0|DR:11|DV:3;test_2_reheader_INFO=Sniffles2.INS.28SF|PRECISE|SVTYPE:INS|SVLEN:81|END:507740|SUPPORT:3|COVERAGE:14:14:14:14:16|STRAND:+|AF:0.214|STDEV_LEN:0|STDEV_POS:0.577|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:0:11:3",
+                "chr16\t507831\tSniffles2.INS.19SF\tN\tTTCAGTATCATCTGCCCGTTCTGAGCCATTTGCTCTCTAGCCCTACCATACAGCTGCCATCCTAAGAGTACGTTTCCCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=81;END=507831;SUPPORT=4;COVERAGE=5,5,5,5,7;STRAND=+-;AF=0.8;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.INS.19SF|chr16;test_1_reheader_POS=Sniffles2.INS.19SF|507831;test_1_reheader_QUAL=Sniffles2.INS.19SF|60;test_1_reheader_FILTERS=Sniffles2.INS.19SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.19SF|test_1|GT:1/1|GQ:1|DR:1|DV:4;test_1_reheader_INFO=Sniffles2.INS.19SF|PRECISE|SVTYPE:INS|SVLEN:81|END:507831|SUPPORT:4|COVERAGE:5:5:5:5:7|STRAND:+-|AF:0.8|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t1/1:1:1:4\t./.:.:.:.",
+                "chr16\t534179\tSniffles2.INS.1ASF:test_1_reheader|Sniffles2.INS.2CSF:test_2_reheader\tN\tGGGCCGTGGTCCTGTCGTGGGAGGCGACGGTGAGGGCGGCCCGGGGTCCCGACGGGGCCGTGGTCCTGTCGTGGGAGGCGACGGTGAGGGCGGCCCGGGGTCCCGACGGGGCCGTGGTCCTGTCGTGGGAGGCGACGGTGAGGGCGGCCCGGGGTCCCGACG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=162;END=534179;SUPPORT=5;COVERAGE=5,5,5,5,4;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.2CSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1ASF|chr16;test_2_reheader_CHROM=Sniffles2.INS.2CSF|chr16;test_1_reheader_POS=Sniffles2.INS.1ASF|534179;test_2_reheader_POS=Sniffles2.INS.2CSF|534179;test_1_reheader_QUAL=Sniffles2.INS.1ASF|60;test_2_reheader_QUAL=Sniffles2.INS.2CSF|60;test_1_reheader_FILTERS=Sniffles2.INS.1ASF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.2CSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.1ASF|test_1|GT:1/1|GQ:13|DR:0|DV:5;test_2_reheader_SAMPLE=Sniffles2.INS.2CSF|test_2|GT:1/1|GQ:11|DR:3|DV:15;test_1_reheader_INFO=Sniffles2.INS.1ASF|PRECISE|SVTYPE:INS|SVLEN:162|END:534179|SUPPORT:5|COVERAGE:5:5:5:5:4|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.2CSF|PRECISE|SVTYPE:INS|SVLEN:216|END:534179|SUPPORT:15|COVERAGE:19:18:18:17:17|STRAND:+-|AF:0.833|STDEV_LEN:18.992|STDEV_POS:1.897|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:13:0:5\t1/1:11:3:15",
+                "chr16\t544781\tSniffles2.INS.1BSF:test_1_reheader|Sniffles2.INS.2DSF:test_2_reheader\tN\tCGTCTCCCCCACGTCGCCTCCCCCCACGTCGCCTCCCCCCACGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGCCGTCTCCCCCACGTCGCCGTCTCCCCCACGTCGCCGTCTCCCCCACGTCGCCGTCTCCCCCACGTCGCCGTCTCCCCCACGTCGCCTCCCCCACGTCGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGTCGCCTCCCCCACGTCGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGCCTCCCCCACGTCGCCTCCCCTCACGTCGCCTCCCCCACGTCGTCGCCTCCCCCACGTCGTCGC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=344;END=544781;SUPPORT=8;COVERAGE=8,8,8,8,8;STRAND=+-;AF=1;STDEV_LEN=4.69;STDEV_POS=25.5;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.2DSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1BSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.2DSF|chr16;test_1_reheader_POS=Sniffles2.INS.1BSF|544781;test_2_reheader_POS=Sniffles2.INS.2DSF|544781;test_1_reheader_QUAL=Sniffles2.INS.1BSF|60;test_2_reheader_QUAL=Sniffles2.INS.2DSF|60;test_1_reheader_FILTERS=Sniffles2.INS.1BSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.2DSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.1BSF|test_1|GT:1/1|GQ:22|DR:0|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.2DSF|test_2|GT:1/1|GQ:21|DR:2|DV:15;test_1_reheader_INFO=Sniffles2.INS.1BSF|IMPRECISE|SVTYPE:INS|SVLEN:344|END:544781|SUPPORT:8|COVERAGE:8:8:8:8:8|STRAND:+-|AF:1|STDEV_LEN:4.69|STDEV_POS:25.5|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.2DSF|IMPRECISE|SVTYPE:INS|SVLEN:348|END:544781|SUPPORT:15|COVERAGE:17:17:17:17:17|STRAND:+-|AF:0.882|STDEV_LEN:5.196|STDEV_POS:28.465|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:22:0:8\t1/1:21:2:15",
+                "chr16\t550769\tSniffles2.INS.1CSF:test_1_reheader|Sniffles2.INS.2ESF:test_2_reheader\tN\tCGGTGAGGGTCCCCGGTCGGTGAGGGCGCCCCGTCAGTGAGGGTCCCGGTCAGTGAGGGCCCCGGTCGGTGAGGGTCCCCGGTCGGTGAGGGCCCCTGTCGGTGAGGGCCCCGGTCGGTGAGGGACCCGGTCGGTGAGGGCCCCCTGTCGGTGAGGGTCCCCTGTCGGTGAGGGCCCCGGTCGGTGAGGGCCCCGGTCGGTGAGGGTCCCCTGTCGGTGAGGGTCCCCTGTCGGTGAGGGTCCCGGTCGGTGAGGGCCCCGGTCGGTGAGGGTGCCCCGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=280;END=550769;SUPPORT=13;COVERAGE=13,13,13,13,13;STRAND=+-;AF=1;STDEV_LEN=1;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.2ESF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1CSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.2ESF|chr16;test_1_reheader_POS=Sniffles2.INS.1CSF|550769;test_2_reheader_POS=Sniffles2.INS.2ESF|550769;test_1_reheader_QUAL=Sniffles2.INS.1CSF|60;test_2_reheader_QUAL=Sniffles2.INS.2ESF|60;test_1_reheader_FILTERS=Sniffles2.INS.1CSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.2ESF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.1CSF|test_1|GT:1/1|GQ:36|DR:0|DV:13;test_2_reheader_SAMPLE=Sniffles2.INS.2ESF|test_2|GT:1/1|GQ:38|DR:2|DV:21;test_1_reheader_INFO=Sniffles2.INS.1CSF|PRECISE|SVTYPE:INS|SVLEN:280|END:550769|SUPPORT:13|COVERAGE:13:13:13:13:13|STRAND:+-|AF:1|STDEV_LEN:1|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.2ESF|PRECISE|SVTYPE:INS|SVLEN:280|END:550769|SUPPORT:21|COVERAGE:23:23:23:23:24|STRAND:+-|AF:0.913|STDEV_LEN:0.65|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:36:0:13\t1/1:38:2:21",
+                "chr16\t553057\tSniffles2.INS.1DSF:test_1_reheader|Sniffles2.INS.2FSF:test_2_reheader\tN\tTGCCCCCCACCCCTGCACAGGTGCCCCCTCCCCTACCCCGCTGCACCCACACCCAACTCGTGCCCCCCCACCCCTGCACAGGTGCCCCCTCCCCTACCCCGCTGCACCCACACCCAACTCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=121;END=553057;SUPPORT=6;COVERAGE=12,11,11,11,10;STRAND=+-;AF=0.545;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.2FSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1DSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.2FSF|chr16;test_1_reheader_POS=Sniffles2.INS.1DSF|553057;test_2_reheader_POS=Sniffles2.INS.2FSF|553059;test_1_reheader_QUAL=Sniffles2.INS.1DSF|60;test_2_reheader_QUAL=Sniffles2.INS.2FSF|60;test_1_reheader_FILTERS=Sniffles2.INS.1DSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.2FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.1DSF|test_1|GT:0/1|GQ:33|DR:5|DV:6;test_2_reheader_SAMPLE=Sniffles2.INS.2FSF|test_2|GT:0/1|GQ:59|DR:11|DV:9;test_1_reheader_INFO=Sniffles2.INS.1DSF|PRECISE|SVTYPE:INS|SVLEN:121|END:553057|SUPPORT:6|COVERAGE:12:11:11:11:10|STRAND:+-|AF:0.545|STDEV_LEN:0.577|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.2FSF|PRECISE|SVTYPE:INS|SVLEN:122|END:553059|SUPPORT:9|COVERAGE:21:20:20:20:19|STRAND:+-|AF:0.45|STDEV_LEN:0.983|STDEV_POS:9.709|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:33:5:6\t0/1:59:11:9",
+                "chr16\t571110\tSniffles2.INS.1FSF:test_1_reheader|Sniffles2.INS.30SF:test_2_reheader\tN\tTGGCTAGCCTGTGTGTGTGTGTGTCTGGCTAGCCTGTGTGTGTGTGTGTGTCTGGCTAGCCTGGTGCCCGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTCTGGCTAGCTGGCGCCCGTGGCTAGCCTGGTGCCCGTGTGTGTGTGTATGTATGTGTCTGGCTAGCCTGGTGCCCGTGGCTAGCCTGGTGCCCGTGTGTGTGTGTGTGGGGGGGGCTAGCCTTGTGTGTGTGTGTCTGGCTAGCCTGTGTGTGTCTGGCTAGCGTGTGTGTGTGTGTCTGGCTAGCCTGTGTGTGTGTGTGTGCTAGCCTGGCGCCCGTGTGTGTGTGTGTGTGTGTCTGGCTAGCCTGGCACCG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=358;END=571110;SUPPORT=16;COVERAGE=18,17,16,16,18;STRAND=+-;AF=1;STDEV_LEN=3.78;STDEV_POS=14.714;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.30SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.1FSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.30SF|chr16;test_1_reheader_POS=Sniffles2.INS.1FSF|571110;test_2_reheader_POS=Sniffles2.INS.30SF|571110;test_1_reheader_QUAL=Sniffles2.INS.1FSF|60;test_2_reheader_QUAL=Sniffles2.INS.30SF|60;test_1_reheader_FILTERS=Sniffles2.INS.1FSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.30SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.1FSF|test_1|GT:1/1|GQ:44|DR:0|DV:16;test_2_reheader_SAMPLE=Sniffles2.INS.30SF|test_2|GT:0/1|GQ:27|DR:5|DV:8;test_1_reheader_INFO=Sniffles2.INS.1FSF|PRECISE|SVTYPE:INS|SVLEN:358|END:571110|SUPPORT:16|COVERAGE:18:17:16:16:18|STRAND:+-|AF:1|STDEV_LEN:3.78|STDEV_POS:14.714|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.30SF|PRECISE|SVTYPE:INS|SVLEN:356|END:571110|SUPPORT:8|COVERAGE:15:13:13:13:13|STRAND:+-|AF:0.615|STDEV_LEN:3.578|STDEV_POS:15.652|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:44:0:16\t0/1:27:5:8",
+                "chr16\t579380\tSniffles2.DEL.62SF\tcagagaagagacagacacacagccccgaaggtggtgcaggcacaggccctagaggtgccccgggcccagagactagagatgccccgggcccggagactagaggtgccccgggcccggaga\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-120;END=579500;SUPPORT=6;COVERAGE=11,11,11,11,10;STRAND=+-;AF=0.545;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.62SF|chr16;test_1_reheader_POS=Sniffles2.DEL.62SF|579380;test_1_reheader_QUAL=Sniffles2.DEL.62SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.62SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.62SF|test_1|GT:0/1|GQ:33|DR:5|DV:6;test_1_reheader_INFO=Sniffles2.DEL.62SF|PRECISE|SVTYPE:DEL|SVLEN:-120|END:579500|SUPPORT:6|COVERAGE:11:11:11:11:10|STRAND:+-|AF:0.545|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:33:5:6\t./.:.:.:.",
+                "chr16\t579477\tSniffles2.DEL.A0SF\ttagaggtgccccgggcccggagactagaggtgccccgggcccggagactagaggtgccccgggcccggagact\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-73;END=579550;SUPPORT=16;COVERAGE=18,18,20,22,22;STRAND=+-;AF=0.8;STDEV_LEN=18.145;STDEV_POS=50.055;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.A0SF|chr16;test_2_reheader_POS=Sniffles2.DEL.A0SF|579477;test_2_reheader_QUAL=Sniffles2.DEL.A0SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.A0SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.A0SF|test_2|GT:1/1|GQ:4|DR:4|DV:16;test_2_reheader_INFO=Sniffles2.DEL.A0SF|IMPRECISE|SVTYPE:DEL|SVLEN:-73|END:579550|SUPPORT:16|COVERAGE:18:18:20:22:22|STRAND:+-|AF:0.8|STDEV_LEN:18.145|STDEV_POS:50.055|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:4:4:16",
+                "chr16\t579636\tSniffles2.DEL.61SF\tcccggagactagaggtgccccgggcccggagactagaggtgccccgggcccggagacttgaggtgccccggg\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-72;END=579708;SUPPORT=5;COVERAGE=11,11,11,10,10;STRAND=+-;AF=0.455;STDEV_LEN=11.5;STDEV_POS=105.434;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.61SF|chr16;test_1_reheader_POS=Sniffles2.DEL.61SF|579636;test_1_reheader_QUAL=Sniffles2.DEL.61SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.61SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.61SF|test_1|GT:0/1|GQ:33|DR:6|DV:5;test_1_reheader_INFO=Sniffles2.DEL.61SF|IMPRECISE|SVTYPE:DEL|SVLEN:-72|END:579708|SUPPORT:5|COVERAGE:11:11:11:10:10|STRAND:+-|AF:0.455|STDEV_LEN:11.5|STDEV_POS:105.434|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:33:6:5\t./.:.:.:.",
+                "chr16\t584946\tSniffles2.DEL.A2SF\tctcccgctccccccagctgcccaccgggtccaccaacacccccaacctgtgcctcccgctccccccagctgcccaccgggtccaccaacacccccaacctgtgcctcccgctccccccagctgcccaccgggtccaccaacacccccaacctgtg\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-155;END=585101;SUPPORT=18;COVERAGE=23,23,23,22,21;STRAND=+-;AF=0.783;STDEV_LEN=0.775;STDEV_POS=76.512;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.A2SF|chr16;test_2_reheader_POS=Sniffles2.DEL.A2SF|584946;test_2_reheader_QUAL=Sniffles2.DEL.A2SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.A2SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.A2SF|test_2|GT:1/1|GQ:0|DR:5|DV:18;test_2_reheader_INFO=Sniffles2.DEL.A2SF|IMPRECISE|SVTYPE:DEL|SVLEN:-155|END:585101|SUPPORT:18|COVERAGE:23:23:23:22:21|STRAND:+-|AF:0.783|STDEV_LEN:0.775|STDEV_POS:76.512|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:0:5:18",
+                "chr16\t585059\tSniffles2.DEL.63SF\tcccccagctgcccaccgggtccaccaacacccccaacctgtgcctcccgctccccccagctgcccaccgggtccaccaacacccccaacctgtgcctcccgctccccccagctgcccaccgggtccaccaacacccccaacctgtgcctcccgctc\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-156;END=585215;SUPPORT=6;COVERAGE=6,6,6,6,6;STRAND=+-;AF=1;STDEV_LEN=0.5;STDEV_POS=56.518;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.63SF|chr16;test_1_reheader_POS=Sniffles2.DEL.63SF|585059;test_1_reheader_QUAL=Sniffles2.DEL.63SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.63SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.63SF|test_1|GT:1/1|GQ:16|DR:0|DV:6;test_1_reheader_INFO=Sniffles2.DEL.63SF|IMPRECISE|SVTYPE:DEL|SVLEN:-156|END:585215|SUPPORT:6|COVERAGE:6:6:6:6:6|STRAND:+-|AF:1|STDEV_LEN:0.5|STDEV_POS:56.518|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t1/1:16:0:6\t./.:.:.:.",
+                "chr16\t587440\tSniffles2.INS.20SF:test_1_reheader|Sniffles2.INS.33SF:test_2_reheader\tN\tTCCCTCCCTTCACTGGGCCTGCTGCCCCAGAGTCCA\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=36;END=587440;SUPPORT=5;COVERAGE=5,5,5,5,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=41.569;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.33SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.20SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.33SF|chr16;test_1_reheader_POS=Sniffles2.INS.20SF|587440;test_2_reheader_POS=Sniffles2.INS.33SF|587440;test_1_reheader_QUAL=Sniffles2.INS.20SF|60;test_2_reheader_QUAL=Sniffles2.INS.33SF|60;test_1_reheader_FILTERS=Sniffles2.INS.20SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.33SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.20SF|test_1|GT:1/1|GQ:13|DR:0|DV:5;test_2_reheader_SAMPLE=Sniffles2.INS.33SF|test_2|GT:1/1|GQ:24|DR:2|DV:16;test_1_reheader_INFO=Sniffles2.INS.20SF|IMPRECISE|SVTYPE:INS|SVLEN:36|END:587440|SUPPORT:5|COVERAGE:5:5:5:5:5|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:41.569|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.33SF|IMPRECISE|SVTYPE:INS|SVLEN:36|END:587440|SUPPORT:16|COVERAGE:20:20:18:17:17|STRAND:+-|AF:0.889|STDEV_LEN:0|STDEV_POS:29.087|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:13:0:5\t1/1:24:2:16",
+                "chr16\t599821\tSniffles2.INS.34SF\tN\tAAGGTTTGTTTCCTCGTGGCATCAGTCAGCGTGGATTGGGCAAGGTTTTGTTCCCTCGTGGCATCAGTCAGCGTGGACG\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=81;END=599821;SUPPORT=9;COVERAGE=10,10,10,10,8;STRAND=+-;AF=0.9;STDEV_LEN=1.169;STDEV_POS=76.821;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.34SF|chr16;test_2_reheader_POS=Sniffles2.INS.34SF|599821;test_2_reheader_QUAL=Sniffles2.INS.34SF|60;test_2_reheader_FILTERS=Sniffles2.INS.34SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.34SF|test_2|GT:1/1|GQ:15|DR:1|DV:9;test_2_reheader_INFO=Sniffles2.INS.34SF|IMPRECISE|SVTYPE:INS|SVLEN:81|END:599821|SUPPORT:9|COVERAGE:10:10:10:10:8|STRAND:+-|AF:0.9|STDEV_LEN:1.169|STDEV_POS:76.821|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:15:1:9",
+                "chr16\t606435\tSniffles2.INS.35SF\tN\tCAGTCCTGCTTTTCTTGGTCCCTCAGTCCAGTGTGGGTTTCCCTGGGCTGAAGTCAAGGTGTTGGCTGACACA\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=66;END=606435;SUPPORT=10;COVERAGE=8,10,10,10,14;STRAND=+-;AF=1;STDEV_LEN=1.225;STDEV_POS=97.931;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.35SF|chr16;test_2_reheader_POS=Sniffles2.INS.35SF|606435;test_2_reheader_QUAL=Sniffles2.INS.35SF|60;test_2_reheader_FILTERS=Sniffles2.INS.35SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.35SF|test_2|GT:1/1|GQ:27|DR:0|DV:10;test_2_reheader_INFO=Sniffles2.INS.35SF|IMPRECISE|SVTYPE:INS|SVLEN:66|END:606435|SUPPORT:10|COVERAGE:8:10:10:10:14|STRAND:+-|AF:1|STDEV_LEN:1.225|STDEV_POS:97.931|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:27:0:10",
+                "chr16\t611747\tSniffles2.DEL.A4SF\tgcctgtagattcaagagcagggacagccgccctggcctgtagaatcaagagcaagggacagccgccttc\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-69;END=611816;SUPPORT=7;COVERAGE=12,12,12,12,12;STRAND=+-;AF=0.583;STDEV_LEN=0;STDEV_POS=49.641;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.A4SF|chr16;test_2_reheader_POS=Sniffles2.DEL.A4SF|611747;test_2_reheader_QUAL=Sniffles2.DEL.A4SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.A4SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.A4SF|test_2|GT:0/1|GQ:30|DR:5|DV:7;test_2_reheader_INFO=Sniffles2.DEL.A4SF|IMPRECISE|SVTYPE:DEL|SVLEN:-69|END:611816|SUPPORT:7|COVERAGE:12:12:12:12:12|STRAND:+-|AF:0.583|STDEV_LEN:0|STDEV_POS:49.641|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:30:5:7",
+                "chr16\t611801\tSniffles2.DEL.64SF:test_1_reheader|Sniffles2.DEL.A8SF:test_2_reheader\tgggacagccgccttcgcctgtagaatcaagagcagggacagccgccctggcctgtagaatcaagagcacgggacagccgccctggcctgtagaatcaagagcacgggacagccgccctggcctgtagaatcaagagcagggacagccgccctggcctgtagaatcaagagcaagggacagccgccctggcctgtagaatcaagagcaagggacagccgcctttgcctgtagaatcaagagcag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-243;END=612044;SUPPORT=4;COVERAGE=3,4,4,4,4;STRAND=+-;AF=1;STDEV_LEN=0.707;STDEV_POS=14.142;FOUND_IN=sniffles;VARID=Sniffles2.DEL.A8SF:test_2_reheader;set=test_1_reheader-filterIntest_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.64SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.A8SF|chr16;test_1_reheader_POS=Sniffles2.DEL.64SF|611801;test_2_reheader_POS=Sniffles2.DEL.A8SF|611793;test_1_reheader_QUAL=Sniffles2.DEL.64SF|60;test_2_reheader_QUAL=Sniffles2.DEL.A8SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.64SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.A8SF|GT;test_1_reheader_SAMPLE=Sniffles2.DEL.64SF|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.DEL.A8SF|test_2|GT:0/0|GQ:7|DR:10|DV:2;test_1_reheader_INFO=Sniffles2.DEL.64SF|PRECISE|SVTYPE:DEL|SVLEN:-243|END:612044|SUPPORT:4|COVERAGE:3:4:4:4:4|STRAND:+-|AF:1|STDEV_LEN:0.707|STDEV_POS:14.142|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.A8SF|PRECISE|SVTYPE:DEL|SVLEN:-242|END:612035|SUPPORT:2|COVERAGE:12:12:12:12:12|STRAND:-|AF:0.167|STDEV_LEN:0.707|STDEV_POS:7.778|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t0/0:7:10:2",
+                "chr16\t611989\tSniffles2.DEL.A5SF\tgcctgtagaatcaagagcaagggacagccgccttt\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-35;END=612024;SUPPORT=4;COVERAGE=12,12,12,12,12;STRAND=+-;AF=0.333;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.A5SF|chr16;test_2_reheader_POS=Sniffles2.DEL.A5SF|611989;test_2_reheader_QUAL=Sniffles2.DEL.A5SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.A5SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.A5SF|test_2|GT:0/1|GQ:17|DR:8|DV:4;test_2_reheader_INFO=Sniffles2.DEL.A5SF|PRECISE|SVTYPE:DEL|SVLEN:-35|END:612024|SUPPORT:4|COVERAGE:12:12:12:12:12|STRAND:+-|AF:0.333|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:17:8:4",
+                "chr16\t612007\tSniffles2.DEL.A6SF\taagggacagccgcctttgcctgtagaatcaagagcagggacagccgccctggcctgtagcatcaagagca\tN\t60\tGT\tIMPRECISE;SVTYPE=DEL;SVLEN=-70;END=612077;SUPPORT=2;COVERAGE=12,12,12,12,12;STRAND=-;AF=0.167;STDEV_LEN=1.414;STDEV_POS=26.87;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.A6SF|chr16;test_2_reheader_POS=Sniffles2.DEL.A6SF|612007;test_2_reheader_QUAL=Sniffles2.DEL.A6SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.A6SF|GT;test_2_reheader_SAMPLE=Sniffles2.DEL.A6SF|test_2|GT:0/0|GQ:7|DR:10|DV:2;test_2_reheader_INFO=Sniffles2.DEL.A6SF|IMPRECISE|SVTYPE:DEL|SVLEN:-70|END:612077|SUPPORT:2|COVERAGE:12:12:12:12:12|STRAND:-|AF:0.167|STDEV_LEN:1.414|STDEV_POS:26.87|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:7:10:2",
+                "chr16\t612374\tSniffles2.DEL.ABSF\tttcaagagcagggacagccgccctggcctgtagaatcaagagcaagggacagccgccttcgcctgtaga\tN\t60\tGT\tPRECISE;SVTYPE=DEL;SVLEN=-69;END=612443;SUPPORT=3;COVERAGE=12,12,12,12,13;STRAND=+-;AF=0.25;STDEV_LEN=0.577;STDEV_POS=5.196;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.ABSF|chr16;test_2_reheader_POS=Sniffles2.DEL.ABSF|612374;test_2_reheader_QUAL=Sniffles2.DEL.ABSF|60;test_2_reheader_FILTERS=Sniffles2.DEL.ABSF|GT;test_2_reheader_SAMPLE=Sniffles2.DEL.ABSF|test_2|GT:0/1|GQ:4|DR:9|DV:3;test_2_reheader_INFO=Sniffles2.DEL.ABSF|PRECISE|SVTYPE:DEL|SVLEN:-69|END:612443|SUPPORT:3|COVERAGE:12:12:12:12:13|STRAND:+-|AF:0.25|STDEV_LEN:0.577|STDEV_POS:5.196|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:4:9:3",
+                "chr16\t612593\tSniffles2.DEL.AFSF:test_2_reheader|Sniffles2.DEL.AESF:test_2_reheader\tggacagccgccctggcctgtagaatcaagagcaagggacagccgcctttgcctgtagaatcaagagcagggacagctgccctggcctgtagcatcaagagca\tN\t60\tGT\tIMPRECISE;SVTYPE=DEL;SVLEN=-102;END=612695;SUPPORT=2;COVERAGE=12,12,12,12,13;STRAND=-;AF=0.167;STDEV_LEN=26.163;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.AESF:test_2_reheader;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.AFSF|chr16,Sniffles2.DEL.AESF|chr16;test_2_reheader_POS=Sniffles2.DEL.AFSF|612593,Sniffles2.DEL.AESF|612625;test_2_reheader_QUAL=Sniffles2.DEL.AFSF|60,Sniffles2.DEL.AESF|60;test_2_reheader_FILTERS=Sniffles2.DEL.AFSF|GT,Sniffles2.DEL.AESF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.AFSF|test_2|GT:0/0|GQ:7|DR:10|DV:2,Sniffles2.DEL.AESF|test_2|GT:0/1|GQ:30|DR:5|DV:7;test_2_reheader_INFO=Sniffles2.DEL.AFSF|IMPRECISE|SVTYPE:DEL|SVLEN:-102|END:612695|SUPPORT:2|COVERAGE:12:12:12:12:13|STRAND:-|AF:0.167|STDEV_LEN:26.163|STDEV_POS:0|FOUND_IN:sniffles,Sniffles2.DEL.AESF|PRECISE|SVTYPE:DEL|SVLEN:-70|END:612695|SUPPORT:7|COVERAGE:12:12:12:12:13|STRAND:+-|AF:0.583|STDEV_LEN:0.894|STDEV_POS:2.683|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:7:10:2",
+                "chr16\t631728\tSniffles2.DEL.65SF:test_1_reheader|Sniffles2.DEL.B3SF:test_2_reheader\tcttctcccaccccttcactgcctctccttccatcctctcctcccaccctctcctcccatccactcctcccatccacttcttccatcct\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-88;END=631816;SUPPORT=17;COVERAGE=17,17,17,17,16;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.B3SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.65SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.B3SF|chr16;test_1_reheader_POS=Sniffles2.DEL.65SF|631728;test_2_reheader_POS=Sniffles2.DEL.B3SF|631728;test_1_reheader_QUAL=Sniffles2.DEL.65SF|60;test_2_reheader_QUAL=Sniffles2.DEL.B3SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.65SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.B3SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.65SF|test_1|GT:1/1|GQ:47|DR:0|DV:17;test_2_reheader_SAMPLE=Sniffles2.DEL.B3SF|test_2|GT:1/1|GQ:39|DR:0|DV:14;test_1_reheader_INFO=Sniffles2.DEL.65SF|PRECISE|SVTYPE:DEL|SVLEN:-88|END:631816|SUPPORT:17|COVERAGE:17:17:17:17:16|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.B3SF|PRECISE|SVTYPE:DEL|SVLEN:-88|END:631816|SUPPORT:14|COVERAGE:13:13:12:14:12|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:47:0:17\t1/1:39:0:14",
+                "chr16\t660943\tSniffles2.INS.23SF:test_1_reheader|Sniffles2.INS.3ASF:test_2_reheader\tN\tCCCCCTGTTCGGCCCCTCCCCAGGCCCCCCCCCGCCCGGCCTCAGGCCCCGCCCCCTGTTCGGCCCCTCCCCAGGCCCGGCCTCAGGCCCCGCCCCCTGTTCGGCCCCTCCCCAG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=115;END=660943;SUPPORT=17;COVERAGE=16,16,15,16,16;STRAND=+-;AF=1;STDEV_LEN=1.803;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.3ASF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.23SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.3ASF|chr16;test_1_reheader_POS=Sniffles2.INS.23SF|660943;test_2_reheader_POS=Sniffles2.INS.3ASF|660943;test_1_reheader_QUAL=Sniffles2.INS.23SF|60;test_2_reheader_QUAL=Sniffles2.INS.3ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.23SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.3ASF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.23SF|test_1|GT:1/1|GQ:47|DR:0|DV:17;test_2_reheader_SAMPLE=Sniffles2.INS.3ASF|test_2|GT:0/1|GQ:15|DR:6|DV:16;test_1_reheader_INFO=Sniffles2.INS.23SF|PRECISE|SVTYPE:INS|SVLEN:115|END:660943|SUPPORT:17|COVERAGE:16:16:15:16:16|STRAND:+-|AF:1|STDEV_LEN:1.803|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.3ASF|IMPRECISE|SVTYPE:INS|SVLEN:111|END:660943|SUPPORT:16|COVERAGE:22:22:22:22:19|STRAND:+-|AF:0.727|STDEV_LEN:9.233|STDEV_POS:23.011|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:47:0:17\t0/1:15:6:16",
+                "chr16\t665215\tSniffles2.DEL.66SF:test_1_reheader|Sniffles2.DEL.B4SF:test_2_reheader\tcctcagtctgcagcctgctagggacgcacggccacactcctgtctttcag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-50;END=665265;SUPPORT=22;COVERAGE=19,21,22,22,21;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.B4SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.66SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.B4SF|chr16;test_1_reheader_POS=Sniffles2.DEL.66SF|665215;test_2_reheader_POS=Sniffles2.DEL.B4SF|665215;test_1_reheader_QUAL=Sniffles2.DEL.66SF|60;test_2_reheader_QUAL=Sniffles2.DEL.B4SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.66SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.B4SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.66SF|test_1|GT:1/1|GQ:60|DR:0|DV:22;test_2_reheader_SAMPLE=Sniffles2.DEL.B4SF|test_2|GT:1/1|GQ:10|DR:4|DV:18;test_1_reheader_INFO=Sniffles2.DEL.66SF|PRECISE|SVTYPE:DEL|SVLEN:-50|END:665265|SUPPORT:22|COVERAGE:19:21:22:22:21|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.B4SF|PRECISE|SVTYPE:DEL|SVLEN:-50|END:665265|SUPPORT:18|COVERAGE:22:22:22:22:22|STRAND:+-|AF:0.818|STDEV_LEN:0|STDEV_POS:2.53|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:60:0:22\t1/1:10:4:18",
+                "chr16\t696679\tSniffles2.INS.24SF:test_1_reheader|Sniffles2.INS.3CSF:test_2_reheader\tN\tCCCACCCCAAAGCCACCATCCGCTCCCACCTCCATAGGGTTGCTGCTGCCCGCCCCTGCCCCCCAGCCCTGTCCCCCCCACCACCCAGCCTGGGCGCACACCCCC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=105;END=696679;SUPPORT=10;COVERAGE=11,10,10,10,10;STRAND=+-;AF=1;STDEV_LEN=0.408;STDEV_POS=1.633;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.3CSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.24SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.3CSF|chr16;test_1_reheader_POS=Sniffles2.INS.24SF|696679;test_2_reheader_POS=Sniffles2.INS.3CSF|696679;test_1_reheader_QUAL=Sniffles2.INS.24SF|60;test_2_reheader_QUAL=Sniffles2.INS.3CSF|60;test_1_reheader_FILTERS=Sniffles2.INS.24SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.3CSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.24SF|test_1|GT:1/1|GQ:27|DR:0|DV:10;test_2_reheader_SAMPLE=Sniffles2.INS.3CSF|test_2|GT:1/1|GQ:14|DR:3|DV:16;test_1_reheader_INFO=Sniffles2.INS.24SF|PRECISE|SVTYPE:INS|SVLEN:105|END:696679|SUPPORT:10|COVERAGE:11:10:10:10:10|STRAND:+-|AF:1|STDEV_LEN:0.408|STDEV_POS:1.633|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.3CSF|PRECISE|SVTYPE:INS|SVLEN:105|END:696679|SUPPORT:16|COVERAGE:19:19:19:19:18|STRAND:+-|AF:0.842|STDEV_LEN:0.833|STDEV_POS:22.394|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:27:0:10\t1/1:14:3:16",
+                "chr16\t746237\tSniffles2.DEL.67SF:test_1_reheader|Sniffles2.DEL.B7SF:test_2_reheader\tgaggtgggttcactgcgggtctgcctggctgggcagcaggagaggaggtgggttcactgcgggtctgcctggctgggcagcaggagaggaggtgggttcactgcaggtctgtctggctgggcagcaggaggggagaggtggggtcactgcgggtctgcagggctgcaggaggggagaggtggggtcactgcaggtctgtctggctgggcagcaggagaggaggtgggttcactgcaggtctgtctgggcgggctgcaggagaggaggtggggtcactgcgggtctgtctgggcgggctgcaggagag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-307;END=746544;SUPPORT=7;COVERAGE=13,13,13,13,11;STRAND=+-;AF=0.538;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.B7SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.67SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.B7SF|chr16;test_1_reheader_POS=Sniffles2.DEL.67SF|746237;test_2_reheader_POS=Sniffles2.DEL.B7SF|746243;test_1_reheader_QUAL=Sniffles2.DEL.67SF|60;test_2_reheader_QUAL=Sniffles2.DEL.B7SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.67SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.B7SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.67SF|test_1|GT:0/1|GQ:40|DR:6|DV:7;test_2_reheader_SAMPLE=Sniffles2.DEL.B7SF|test_2|GT:0/1|GQ:18|DR:15|DV:6;test_1_reheader_INFO=Sniffles2.DEL.67SF|PRECISE|SVTYPE:DEL|SVLEN:-307|END:746544|SUPPORT:7|COVERAGE:13:13:13:13:11|STRAND:+-|AF:0.538|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.B7SF|PRECISE|SVTYPE:DEL|SVLEN:-306|END:746549|SUPPORT:6|COVERAGE:21:21:21:21:21|STRAND:+-|AF:0.286|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:40:6:7\t0/1:18:15:6",
+                "chr16\t760502\tSniffles2.INS.25SF:test_1_reheader|Sniffles2.INS.3ESF:test_2_reheader\tN\tAGCCATGAAACCTGGGCCCGGGCTCCCACTCACACCCCACCCCCACCCAGGGCAGCCGTGAAACCTGGGCCCTGGGCTCCCACCCACGCCCCACACCCACCCAGGGC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=107;END=760502;SUPPORT=16;COVERAGE=16,16,16,16,17;STRAND=+-;AF=1;STDEV_LEN=0.518;STDEV_POS=11.667;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.3ESF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.25SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.3ESF|chr16;test_1_reheader_POS=Sniffles2.INS.25SF|760502;test_2_reheader_POS=Sniffles2.INS.3ESF|760502;test_1_reheader_QUAL=Sniffles2.INS.25SF|60;test_2_reheader_QUAL=Sniffles2.INS.3ESF|60;test_1_reheader_FILTERS=Sniffles2.INS.25SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.3ESF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.25SF|test_1|GT:1/1|GQ:44|DR:0|DV:16;test_2_reheader_SAMPLE=Sniffles2.INS.3ESF|test_2|GT:1/1|GQ:32|DR:2|DV:19;test_1_reheader_INFO=Sniffles2.INS.25SF|PRECISE|SVTYPE:INS|SVLEN:107|END:760502|SUPPORT:16|COVERAGE:16:16:16:16:17|STRAND:+-|AF:1|STDEV_LEN:0.518|STDEV_POS:11.667|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.3ESF|PRECISE|SVTYPE:INS|SVLEN:107|END:760502|SUPPORT:19|COVERAGE:20:20:21:21:23|STRAND:+-|AF:0.905|STDEV_LEN:0.674|STDEV_POS:4.221|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:44:0:16\t1/1:32:2:19",
+                "chr16\t763776\tSniffles2.INS.26SF:test_1_reheader|Sniffles2.INS.3FSF:test_2_reheader\tN\tGCATCCCATCCCCCGTCCCCTCCCCCACACCCCTCCCCCACCCCCACGTCCCCTCCCCACCCCTCCCCCACACCCTCCCCCACCCCTCCCCATGTCCCCTCCCCTACCTCCTCCCCCCGCATCCCCTCCCCCC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=133;END=763776;SUPPORT=20;COVERAGE=19,19,20,20,20;STRAND=+-;AF=1;STDEV_LEN=0.789;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.3FSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.26SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.3FSF|chr16;test_1_reheader_POS=Sniffles2.INS.26SF|763776;test_2_reheader_POS=Sniffles2.INS.3FSF|763776;test_1_reheader_QUAL=Sniffles2.INS.26SF|60;test_2_reheader_QUAL=Sniffles2.INS.3FSF|60;test_1_reheader_FILTERS=Sniffles2.INS.26SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.3FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.26SF|test_1|GT:1/1|GQ:55|DR:0|DV:20;test_2_reheader_SAMPLE=Sniffles2.INS.3FSF|test_2|GT:1/1|GQ:48|DR:1|DV:21;test_1_reheader_INFO=Sniffles2.INS.26SF|PRECISE|SVTYPE:INS|SVLEN:133|END:763776|SUPPORT:20|COVERAGE:19:19:20:20:20|STRAND:+-|AF:1|STDEV_LEN:0.789|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.3FSF|PRECISE|SVTYPE:INS|SVLEN:133|END:763776|SUPPORT:21|COVERAGE:22:22:22:22:23|STRAND:+-|AF:0.955|STDEV_LEN:1.092|STDEV_POS:1.391|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:55:0:20\t1/1:48:1:21",
+                "chr16\t767712\tSniffles2.INS.2ASF\tN\tGCGCATGGGGGGCGTGGGAGGGGGGTGCGTGGAGGAGGGGCGGTGTGGAGGGGGGCGCGTGGGGGTGTGTGGGGGGGGCACGTGGAGGGGGGCGTGTGGGGGGGTGCGTGGAGGAGGGGCGCGTGGAGGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=130;END=767712;SUPPORT=5;COVERAGE=15,15,15,15,14;STRAND=+-;AF=0.333;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.INS.2ASF|chr16;test_1_reheader_POS=Sniffles2.INS.2ASF|767712;test_1_reheader_QUAL=Sniffles2.INS.2ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.2ASF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2ASF|test_1|GT:0/1|GQ:22|DR:10|DV:5;test_1_reheader_INFO=Sniffles2.INS.2ASF|PRECISE|SVTYPE:INS|SVLEN:130|END:767712|SUPPORT:5|COVERAGE:15:15:15:15:14|STRAND:+-|AF:0.333|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:22:10:5\t./.:.:.:.",
+                "chr16\t767829\tSniffles2.INS.29SF:test_1_reheader|Sniffles2.INS.41SF:test_2_reheader\tN\tGGTGTGGAGGGGGGCGCGTGGGGGTGTGTGGGGGGGGGCACGTGGAGGGGGCGTGTGGGGGGGTGCGTGGAGGAGGGGCGCGTGGAGGA\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=89;END=767829;SUPPORT=9;COVERAGE=15,15,15,15,14;STRAND=+-;AF=0.6;STDEV_LEN=3.715;STDEV_POS=36.697;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.41SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.29SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.41SF|chr16;test_1_reheader_POS=Sniffles2.INS.29SF|767829;test_2_reheader_POS=Sniffles2.INS.41SF|767868;test_1_reheader_QUAL=Sniffles2.INS.29SF|60;test_2_reheader_QUAL=Sniffles2.INS.41SF|60;test_1_reheader_FILTERS=Sniffles2.INS.29SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.41SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.29SF|test_1|GT:0/1|GQ:34|DR:6|DV:9;test_2_reheader_SAMPLE=Sniffles2.INS.41SF|test_2|GT:0/1|GQ:16|DR:12|DV:5;test_1_reheader_INFO=Sniffles2.INS.29SF|IMPRECISE|SVTYPE:INS|SVLEN:89|END:767829|SUPPORT:9|COVERAGE:15:15:15:15:14|STRAND:+-|AF:0.6|STDEV_LEN:3.715|STDEV_POS:36.697|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.41SF|IMPRECISE|SVTYPE:INS|SVLEN:135|END:767868|SUPPORT:5|COVERAGE:23:16:17:16:17|STRAND:+-|AF:0.294|STDEV_LEN:3.215|STDEV_POS:90.067|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:34:6:9\t0/1:16:12:5",
+                "chr16\t767989\tSniffles2.INS.28SF:test_1_reheader|Sniffles2.INS.40SF:test_2_reheader\tN\tGGGGCACATGGGGGTGCGTGGGGGGCGTGTGGGGGGTGCGTGGAGGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=47;END=767989;SUPPORT=6;COVERAGE=15,15,15,14,14;STRAND=+-;AF=0.4;STDEV_LEN=1.5;STDEV_POS=11.547;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.40SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.28SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.40SF|chr16;test_1_reheader_POS=Sniffles2.INS.28SF|767989;test_2_reheader_POS=Sniffles2.INS.40SF|767969;test_1_reheader_QUAL=Sniffles2.INS.28SF|60;test_2_reheader_QUAL=Sniffles2.INS.40SF|60;test_1_reheader_FILTERS=Sniffles2.INS.28SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.40SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.28SF|test_1|GT:0/1|GQ:34|DR:9|DV:6;test_2_reheader_SAMPLE=Sniffles2.INS.40SF|test_2|GT:0/1|GQ:6|DR:4|DV:12;test_1_reheader_INFO=Sniffles2.INS.28SF|PRECISE|SVTYPE:INS|SVLEN:47|END:767989|SUPPORT:6|COVERAGE:15:15:15:14:14|STRAND:+-|AF:0.4|STDEV_LEN:1.5|STDEV_POS:11.547|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.40SF|IMPRECISE|SVTYPE:INS|SVLEN:45|END:767969|SUPPORT:12|COVERAGE:21:17:16:16:17|STRAND:+-|AF:0.75|STDEV_LEN:16.098|STDEV_POS:66.865|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:34:9:6\t0/1:6:4:12",
+                "chr16\t769171\tSniffles2.INS.2BSF:test_1_reheader|Sniffles2.INS.42SF:test_2_reheader\tN\tCCCCGGCCCCGGCCCCAGCCCCGGCCCCACCCCGGCCCCAGCCCCAGCCCCAGCCCCAGCCCCACCCCCGGCCCCAGCCCCAGCCCCAGCCCCAGCCCCGGCCCCACCCCCACCCCCGGCCCCGGCCCCGGCCCCACCCCCGGCCCCGGCCCCGGCCCCACCCCCGGCCCCGGCCCCACCCCCGGCCCCGGCCCCAC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=197;END=769171;SUPPORT=6;COVERAGE=14,13,13,13,13;STRAND=+-;AF=0.462;STDEV_LEN=0.816;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.42SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.2BSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.42SF|chr16;test_1_reheader_POS=Sniffles2.INS.2BSF|769171;test_2_reheader_POS=Sniffles2.INS.42SF|769187;test_1_reheader_QUAL=Sniffles2.INS.2BSF|60;test_2_reheader_QUAL=Sniffles2.INS.42SF|60;test_1_reheader_FILTERS=Sniffles2.INS.2BSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.42SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2BSF|test_1|GT:0/1|GQ:40|DR:7|DV:6;test_2_reheader_SAMPLE=Sniffles2.INS.42SF|test_2|GT:0/1|GQ:52|DR:10|DV:8;test_1_reheader_INFO=Sniffles2.INS.2BSF|PRECISE|SVTYPE:INS|SVLEN:197|END:769171|SUPPORT:6|COVERAGE:14:13:13:13:13|STRAND:+-|AF:0.462|STDEV_LEN:0.816|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.42SF|PRECISE|SVTYPE:INS|SVLEN:193|END:769187|SUPPORT:8|COVERAGE:17:18:18:18:18|STRAND:+-|AF:0.444|STDEV_LEN:0.577|STDEV_POS:5|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:40:7:6\t0/1:52:10:8",
+                "chr16\t795446\tSniffles2.INS.2CSF:test_1_reheader|Sniffles2.INS.44SF:test_2_reheader\tN\tCCCCCGTGCTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCGCCCCCCTGTGCTGCCCGTGTGGCTGCCCCCGGCCCCGCGCCCTTCT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=87;END=795446;SUPPORT=8;COVERAGE=13,13,13,13,13;STRAND=+-;AF=0.615;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.44SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.2CSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.44SF|chr16;test_1_reheader_POS=Sniffles2.INS.2CSF|795446;test_2_reheader_POS=Sniffles2.INS.44SF|795446;test_1_reheader_QUAL=Sniffles2.INS.2CSF|60;test_2_reheader_QUAL=Sniffles2.INS.44SF|60;test_1_reheader_FILTERS=Sniffles2.INS.2CSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.44SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2CSF|test_1|GT:0/1|GQ:27|DR:5|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.44SF|test_2|GT:0/1|GQ:39|DR:11|DV:7;test_1_reheader_INFO=Sniffles2.INS.2CSF|PRECISE|SVTYPE:INS|SVLEN:87|END:795446|SUPPORT:8|COVERAGE:13:13:13:13:13|STRAND:+-|AF:0.615|STDEV_LEN:0.577|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.44SF|PRECISE|SVTYPE:INS|SVLEN:86|END:795446|SUPPORT:7|COVERAGE:20:18:18:18:18|STRAND:+-|AF:0.389|STDEV_LEN:0.816|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:27:5:8\t0/1:39:11:7",
+                "chr16\t795594\tSniffles2.INS.2DSF:test_1_reheader|Sniffles2.INS.46SF:test_2_reheader\tN\tGCTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCCCCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCTTCTCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCGCCCCCCCAAACACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCGCCCCCCCAAACACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCTTCTCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCGCCCCCCCAAACACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCGCCCCCCTGTGCTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCCTCCCCCCAAACACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCCCCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCTTCTCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCCCCCCCAACCACACTGCCCGTGTGGCTGCCCCCGGCCCCGTGCCGCCCCGCCCCGCCCCTCCCCTCCCCCCCCCCCGC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=621;END=795594;SUPPORT=5;COVERAGE=13,13,13,13,13;STRAND=+-;AF=0.385;STDEV_LEN=2.646;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.46SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.2DSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.46SF|chr16;test_1_reheader_POS=Sniffles2.INS.2DSF|795594;test_2_reheader_POS=Sniffles2.INS.46SF|795594;test_1_reheader_QUAL=Sniffles2.INS.2DSF|60;test_2_reheader_QUAL=Sniffles2.INS.46SF|60;test_1_reheader_FILTERS=Sniffles2.INS.2DSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.46SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2DSF|test_1|GT:0/1|GQ:27|DR:8|DV:5;test_2_reheader_SAMPLE=Sniffles2.INS.46SF|test_2|GT:0/1|GQ:26|DR:12|DV:6;test_1_reheader_INFO=Sniffles2.INS.2DSF|PRECISE|SVTYPE:INS|SVLEN:621|END:795594|SUPPORT:5|COVERAGE:13:13:13:13:13|STRAND:+-|AF:0.385|STDEV_LEN:2.646|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.46SF|PRECISE|SVTYPE:INS|SVLEN:617|END:795594|SUPPORT:6|COVERAGE:20:18:18:18:18|STRAND:+-|AF:0.333|STDEV_LEN:2.5|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:27:8:5\t0/1:26:12:6",
+                "chr16\t818868\tSniffles2.INS.2ESF:test_1_reheader|Sniffles2.INS.47SF:test_2_reheader\tN\tTGGTGAAGACTGTAGTGATGGTGATGATGGTGAAGACTGTAGTGATGATGGTGGTGAAGACTGTAGTGATGTTGATATTGGTGATGAAGACTATAGTGATAGTGAAGACTATCGTGATGGTGATGATGATGGTGAAGACTAGTGATGGTGATGATGATGGTGAAGACTGTAGTGATGGTGATGATGGTGAAGACTGTAGCGATGATGGTGAACACTGTAGTGATGTTGATATTGGTGATGAAGACTATAGTGATGGTGATGATAGTGAAGACTATCGTGATGGTGATGATGATGGTGAAGACTGTAGTGATGGTGATGAGGTGAGACTATCGTGATGGTGATGATAATGGTGAAGACTATAGTGATGTTGATGTCGGTGGTGAAGACTGTAGTGATGGTGATGATAGTGAAGACTATCGTGATGGTGATGATGATGGTGAAGACTGTAGTGATGGTGATGATGGTGAAGACTATCGTGATGGTGATGATGATGGTGAAGACTATAGTGATGATGGTGAAGACTGTAGTGATGGTGATGATAGTGGTGAAGACTGTAGTGATGTTAATGGTGAAGGCTATAGTGATGTTGATGGTGGTGAAGACTGTAGCAATGGTTATGATGTTGGTGAAGACAATAGTGATGGTGATGATGGTGAAGACTATAGTGATGGTGATGATGGTGGTGAAGACTGTAGTGATGGTGATGATAGTGGTGAGGACTGTTAGTGATGATAGTGGTGAAGACTGTAGTGATGATGATGGTGAAGACTATAATGATGATGGTGAAGACCGCCGTGATGGTGATGATGGTGAAGACTGTAGCAATGATGATGGTGAAGACTATAGTGATGTTGAGTTGGTGGTGAAGACTGTAGCGATGGTGATGATGATGGTGAAGACTATAGTGATGATGATGTTGAAGACTATAGTGATGATGATGGTGAAGACCGCCGTGATGGTGATGATGGTGAAGACTGTAGCGATGATGATGGTGAAGACTATAGTGATGCTGATGTTGGTGGTGAAGACTGTAGTGATGGTGATGATGATGGTGAAGACTATAGTGATGATGATGGTGAAGACTATAGTGATGATGATGTGAAGACCGCCGTGATGGTGATGATGGTGAAGACTGTAGCGATGATGATGGTGAAGACTATAGTGATGTTGATGTTGG\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=1173;END=818868;SUPPORT=12;COVERAGE=13,12,12,12,12;STRAND=+-;AF=1;STDEV_LEN=90.396;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.47SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.2ESF|chr16;test_2_reheader_CHROM=Sniffles2.INS.47SF|chr16;test_1_reheader_POS=Sniffles2.INS.2ESF|818868;test_2_reheader_POS=Sniffles2.INS.47SF|818868;test_1_reheader_QUAL=Sniffles2.INS.2ESF|60;test_2_reheader_QUAL=Sniffles2.INS.47SF|60;test_1_reheader_FILTERS=Sniffles2.INS.2ESF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.47SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2ESF|test_1|GT:1/1|GQ:33|DR:0|DV:12;test_2_reheader_SAMPLE=Sniffles2.INS.47SF|test_2|GT:1/1|GQ:5|DR:2|DV:9;test_1_reheader_INFO=Sniffles2.INS.2ESF|IMPRECISE|SVTYPE:INS|SVLEN:1173|END:818868|SUPPORT:12|COVERAGE:13:12:12:12:12|STRAND:+-|AF:1|STDEV_LEN:90.396|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.47SF|IMPRECISE|SVTYPE:INS|SVLEN:1180|END:818868|SUPPORT:9|COVERAGE:14:11:11:11:11|STRAND:+-|AF:0.818|STDEV_LEN:66.808|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:33:0:12\t1/1:5:2:9",
+                "chr16\t824382\tSniffles2.INS.2FSF:test_1_reheader|Sniffles2.INS.48SF:test_2_reheader|Sniffles2.INS.49SF:test_2_reheader\tN\tTAGGCCCACGACGGCCAGCAGCGGGGGAGCTCGTCACACTAGGCCCACGACGGCCAGCAGCGGGGGAGCTCGTCACACTAGGCCCACGACGGCCAGCAGCGGGGGGAGCTCGTCACACTAGGCCCACGACGGCCAGCAGCGGGGGGAGCT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=150;END=824382;SUPPORT=2;COVERAGE=3,3,3,3,2;STRAND=-;AF=0.667;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.48SF:test_2_reheader|Sniffles2.INS.49SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.2FSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.48SF|chr16,Sniffles2.INS.49SF|chr16;test_1_reheader_POS=Sniffles2.INS.2FSF|824382;test_2_reheader_POS=Sniffles2.INS.48SF|824382,Sniffles2.INS.49SF|824382;test_1_reheader_QUAL=Sniffles2.INS.2FSF|60;test_2_reheader_QUAL=Sniffles2.INS.48SF|60,Sniffles2.INS.49SF|60;test_1_reheader_FILTERS=Sniffles2.INS.2FSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.48SF|GT,Sniffles2.INS.49SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.2FSF|test_1|GT:0/1|GQ:4|DR:1|DV:2;test_2_reheader_SAMPLE=Sniffles2.INS.48SF|test_2|GT:0/1|GQ:3|DR:6|DV:2,Sniffles2.INS.49SF|test_2|GT:0/1|GQ:28|DR:4|DV:4;test_1_reheader_INFO=Sniffles2.INS.2FSF|PRECISE|SVTYPE:INS|SVLEN:150|END:824382|SUPPORT:2|COVERAGE:3:3:3:3:2|STRAND:-|AF:0.667|STDEV_LEN:0.707|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.48SF|PRECISE|SVTYPE:INS|SVLEN:152|END:824382|SUPPORT:2|COVERAGE:9:8:8:8:8|STRAND:+|AF:0.25|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.49SF|PRECISE|SVTYPE:INS|SVLEN:475|END:824382|SUPPORT:4|COVERAGE:9:8:8:8:8|STRAND:+-|AF:0.5|STDEV_LEN:4.031|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:4:1:2\t0/1:28:4:4",
+                "chr16\t824874\tSniffles2.INS.31SF:test_1_reheader|Sniffles2.INS.4ASF:test_2_reheader\tN\tCGTCCCGTCCGCGGCACCACCGTCCCATCTGTGGCACCAT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=40;END=824874;SUPPORT=2;COVERAGE=3,2,2,2,2;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.4ASF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.31SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.4ASF|chr16;test_1_reheader_POS=Sniffles2.INS.31SF|824874;test_2_reheader_POS=Sniffles2.INS.4ASF|824874;test_1_reheader_QUAL=Sniffles2.INS.31SF|60;test_2_reheader_QUAL=Sniffles2.INS.4ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.31SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.4ASF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.31SF|test_1|GT:1/1|GQ:5|DR:0|DV:2;test_2_reheader_SAMPLE=Sniffles2.INS.4ASF|test_2|GT:0/1|GQ:3|DR:2|DV:6;test_1_reheader_INFO=Sniffles2.INS.31SF|PRECISE|SVTYPE:INS|SVLEN:40|END:824874|SUPPORT:2|COVERAGE:3:2:2:2:2|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.4ASF|PRECISE|SVTYPE:INS|SVLEN:40|END:824874|SUPPORT:6|COVERAGE:8:8:8:8:8|STRAND:+-|AF:0.75|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:5:0:2\t0/1:3:2:6",
+                "chr16\t828085\tSniffles2.INS.4BSF\tN\tCCGGGGGAAATGAACTCTCGGCCTCCAGGGCAGCCAGGCAGGGGTCTGGCCCAGTCCTCA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=58;END=828085;SUPPORT=4;COVERAGE=8,8,8,8,8;STRAND=+-;AF=0.5;STDEV_LEN=1.5;STDEV_POS=22.765;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.4BSF|chr16;test_2_reheader_POS=Sniffles2.INS.4BSF|828085;test_2_reheader_QUAL=Sniffles2.INS.4BSF|60;test_2_reheader_FILTERS=Sniffles2.INS.4BSF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.4BSF|test_2|GT:0/1|GQ:28|DR:4|DV:4;test_2_reheader_INFO=Sniffles2.INS.4BSF|PRECISE|SVTYPE:INS|SVLEN:58|END:828085|SUPPORT:4|COVERAGE:8:8:8:8:8|STRAND:+-|AF:0.5|STDEV_LEN:1.5|STDEV_POS:22.765|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:28:4:4",
+                "chr16\t828906\tSniffles2.DEL.68SF:test_1_reheader|Sniffles2.DEL.BBSF:test_2_reheader\tgcccactggggcccacatcccgcccactgggaccgacatccc\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-42;END=828948;SUPPORT=2;COVERAGE=2,2,2,2,2;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.BBSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.68SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.BBSF|chr16;test_1_reheader_POS=Sniffles2.DEL.68SF|828906;test_2_reheader_POS=Sniffles2.DEL.BBSF|828906;test_1_reheader_QUAL=Sniffles2.DEL.68SF|60;test_2_reheader_QUAL=Sniffles2.DEL.BBSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.68SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.BBSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.68SF|test_1|GT:1/1|GQ:5|DR:0|DV:2;test_2_reheader_SAMPLE=Sniffles2.DEL.BBSF|test_2|GT:0/1|GQ:3|DR:2|DV:6;test_1_reheader_INFO=Sniffles2.DEL.68SF|PRECISE|SVTYPE:DEL|SVLEN:-42|END:828948|SUPPORT:2|COVERAGE:2:2:2:2:2|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.BBSF|PRECISE|SVTYPE:DEL|SVLEN:-42|END:828948|SUPPORT:6|COVERAGE:8:8:8:8:8|STRAND:+-|AF:0.75|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:5:0:2\t0/1:3:2:6",
+                "chr16\t886663\tSniffles2.INS.35SF:test_1_reheader|Sniffles2.INS.34SF:test_1_reheader|Sniffles2.INS.4DSF:test_2_reheader\tN\tCCACCCTAGGCCCCCGGCGTTCCCCAGGCCCCTCCCACCCTAGGCCCCCGGCGTTCCCCAGGCCCCTCCCACCCTAGGCCCCCGGCGTTCCCCAGGCCCCTCCCACCCTAGGCCCCGGCGTTCCCCAGGCCCCT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=134;END=886663;SUPPORT=8;COVERAGE=10,10,10,10,11;STRAND=+-;AF=0.8;STDEV_LEN=0.5;STDEV_POS=22.234;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.34SF:test_1_reheader|Sniffles2.INS.4DSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.35SF|chr16,Sniffles2.INS.34SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.4DSF|chr16;test_1_reheader_POS=Sniffles2.INS.35SF|886663,Sniffles2.INS.34SF|886674;test_2_reheader_POS=Sniffles2.INS.4DSF|886701;test_1_reheader_QUAL=Sniffles2.INS.35SF|60,Sniffles2.INS.34SF|60;test_2_reheader_QUAL=Sniffles2.INS.4DSF|60;test_1_reheader_FILTERS=Sniffles2.INS.35SF|PASS,Sniffles2.INS.34SF|GT;test_2_reheader_FILTERS=Sniffles2.INS.4DSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.35SF|test_1|GT:1/1|GQ:2|DR:2|DV:8,Sniffles2.INS.34SF|test_1|GT:0/0|GQ:2|DR:8|DV:2;test_2_reheader_SAMPLE=Sniffles2.INS.4DSF|test_2|GT:0/1|GQ:12|DR:4|DV:10;test_1_reheader_INFO=Sniffles2.INS.35SF|PRECISE|SVTYPE:INS|SVLEN:134|END:886663|SUPPORT:8|COVERAGE:10:10:10:10:11|STRAND:+-|AF:0.8|STDEV_LEN:0.5|STDEV_POS:22.234|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.34SF|IMPRECISE|SVTYPE:INS|SVLEN:66|END:886674|SUPPORT:2|COVERAGE:10:10:10:10:11|STRAND:+-|AF:0.2|STDEV_LEN:19.348|STDEV_POS:113.694|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.4DSF|IMPRECISE|SVTYPE:INS|SVLEN:131|END:886701|SUPPORT:10|COVERAGE:14:14:14:14:14|STRAND:+-|AF:0.714|STDEV_LEN:16.561|STDEV_POS:60.663|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:2:2:8\t0/1:12:4:10",
+                "chr16\t894215\tSniffles2.INS.36SF:test_1_reheader|Sniffles2.INS.53SF:test_2_reheader\tN\tCTGGCTGTCCGCCCACCCATCCCCTGTCCACCGGACCGTCCGCCCACCCGTCCCCATGTCCATCAGACCGTCCGTCCACCTGTCCCCCTGTCCCCTGTCCACCGGACCATTCGCCCACCCATCCCCCTGTCCACCTGGCCATCCGCCCACCTGTCTCCTGTCCACCGGACCGTCCACCCACCCGTCCCCCTGTCCACCGGACCGTCCACCCACCCGTCCCCCTGTCCACTGGACTGTCCGCCCACCTGTCCCCCTGTCCCCTGTCCACCGGACCGTCTGCCCACCCGTCCCCCTGTCCACCTGGCCATCCGCCCACCCATCCCTGTCCACCGGACCGTCCACCCACCCGTCCCCCTGTCCAGGTCCCCCTGTCCAGCGGACCGTCCACCCACCCGTCCCCCTGTCCACTGGACCGTCCGCCCACCTGTCCCCCTGTCCACCTGGCAGTGCGCCCACCCATCCCCTGTCCACCGGACCGTCCACCCACCCGTCCCCCTGTCCAGCGGACCGTCCACCCACCT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=521;END=894215;SUPPORT=17;COVERAGE=17,17,17,17,17;STRAND=+-;AF=1;STDEV_LEN=57.393;STDEV_POS=5.5;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.53SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.36SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.53SF|chr16;test_1_reheader_POS=Sniffles2.INS.36SF|894215;test_2_reheader_POS=Sniffles2.INS.53SF|894226;test_1_reheader_QUAL=Sniffles2.INS.36SF|60;test_2_reheader_QUAL=Sniffles2.INS.53SF|60;test_1_reheader_FILTERS=Sniffles2.INS.36SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.53SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.36SF|test_1|GT:1/1|GQ:47|DR:0|DV:17;test_2_reheader_SAMPLE=Sniffles2.INS.53SF|test_2|GT:0/1|GQ:54|DR:8|DV:9;test_1_reheader_INFO=Sniffles2.INS.36SF|IMPRECISE|SVTYPE:INS|SVLEN:521|END:894215|SUPPORT:17|COVERAGE:17:17:17:17:17|STRAND:+-|AF:1|STDEV_LEN:57.393|STDEV_POS:5.5|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.53SF|IMPRECISE|SVTYPE:INS|SVLEN:532|END:894226|SUPPORT:9|COVERAGE:17:17:17:17:17|STRAND:+-|AF:0.529|STDEV_LEN:71.587|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:47:0:17\t0/1:54:8:9",
+                "chr16\t895843\tSniffles2.INS.37SF:test_1_reheader|Sniffles2.INS.39SF:test_1_reheader|Sniffles2.INS.57SF:test_2_reheader|Sniffles2.INS.55SF:test_2_reheader\tN\tACACGCCTCGGAGGGGTTGTGAGGCTCAGCCACCCACACGCAGGCTGCACGGTCCACAG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=59;END=895843;SUPPORT=4;COVERAGE=17,16,16,16,14;STRAND=+-;AF=0.25;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.39SF:test_1_reheader|Sniffles2.INS.57SF:test_2_reheader|Sniffles2.INS.55SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.37SF|chr16,Sniffles2.INS.39SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.57SF|chr16,Sniffles2.INS.55SF|chr16;test_1_reheader_POS=Sniffles2.INS.37SF|895843,Sniffles2.INS.39SF|895843;test_2_reheader_POS=Sniffles2.INS.57SF|895843,Sniffles2.INS.55SF|895870;test_1_reheader_QUAL=Sniffles2.INS.37SF|60,Sniffles2.INS.39SF|60;test_2_reheader_QUAL=Sniffles2.INS.57SF|60,Sniffles2.INS.55SF|60;test_1_reheader_FILTERS=Sniffles2.INS.37SF|PASS,Sniffles2.INS.39SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.57SF|PASS,Sniffles2.INS.55SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.37SF|test_1|GT:0/1|GQ:6|DR:12|DV:4,Sniffles2.INS.39SF|test_1|GT:0/1|GQ:57|DR:8|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.57SF|test_2|GT:0/1|GQ:34|DR:9|DV:6,Sniffles2.INS.55SF|test_2|GT:0/1|GQ:22|DR:10|DV:5;test_1_reheader_INFO=Sniffles2.INS.37SF|PRECISE|SVTYPE:INS|SVLEN:59|END:895843|SUPPORT:4|COVERAGE:17:16:16:16:14|STRAND:+-|AF:0.25|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.39SF|PRECISE|SVTYPE:INS|SVLEN:177|END:895843|SUPPORT:8|COVERAGE:17:16:16:16:14|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.57SF|PRECISE|SVTYPE:INS|SVLEN:177|END:895843|SUPPORT:6|COVERAGE:15:15:15:15:15|STRAND:+-|AF:0.4|STDEV_LEN:1.949|STDEV_POS:8.944|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.55SF|PRECISE|SVTYPE:INS|SVLEN:59|END:895870|SUPPORT:5|COVERAGE:15:15:15:15:15|STRAND:+-|AF:0.333|STDEV_LEN:0|STDEV_POS:15.588|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:6:12:4\t0/1:22:10:5",
+                "chr16\t896053\tSniffles2.INS.3BSF:test_1_reheader|Sniffles2.INS.3ASF:test_1_reheader|Sniffles2.INS.56SF:test_2_reheader\tN\tCCACACGCAGGCTGCACGGTCCACAGACACGCCTCGGAGGGGTTGTGAGGCTCAGCCACCCACACGCAGGCTGCACGGTCCACACACACGCCTCGGAGGGGTTGTGAGGCTCAGCCAT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=118;END=896053;SUPPORT=8;COVERAGE=17,16,16,16,14;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.3ASF:test_1_reheader|Sniffles2.INS.56SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.3BSF|chr16,Sniffles2.INS.3ASF|chr16;test_2_reheader_CHROM=Sniffles2.INS.56SF|chr16;test_1_reheader_POS=Sniffles2.INS.3BSF|896053,Sniffles2.INS.3ASF|896059;test_2_reheader_POS=Sniffles2.INS.56SF|896053;test_1_reheader_QUAL=Sniffles2.INS.3BSF|60,Sniffles2.INS.3ASF|60;test_2_reheader_QUAL=Sniffles2.INS.56SF|60;test_1_reheader_FILTERS=Sniffles2.INS.3BSF|PASS,Sniffles2.INS.3ASF|GT;test_2_reheader_FILTERS=Sniffles2.INS.56SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.3BSF|test_1|GT:0/1|GQ:57|DR:8|DV:8,Sniffles2.INS.3ASF|test_1|GT:0/0|GQ:6|DR:13|DV:3;test_2_reheader_SAMPLE=Sniffles2.INS.56SF|test_2|GT:0/1|GQ:34|DR:9|DV:6;test_1_reheader_INFO=Sniffles2.INS.3BSF|PRECISE|SVTYPE:INS|SVLEN:118|END:896053|SUPPORT:8|COVERAGE:17:16:16:16:14|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.3ASF|IMPRECISE|SVTYPE:INS|SVLEN:58|END:896059|SUPPORT:3|COVERAGE:17:16:16:16:14|STRAND:+-|AF:0.188|STDEV_LEN:0.577|STDEV_POS:38.553|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.56SF|IMPRECISE|SVTYPE:INS|SVLEN:118|END:896053|SUPPORT:6|COVERAGE:15:15:15:15:15|STRAND:+-|AF:0.4|STDEV_LEN:0.447|STDEV_POS:64.631|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:57:8:8\t0/1:34:9:6",
+                "chr16\t903595\tSniffles2.INS.3ESF:test_1_reheader|Sniffles2.INS.5ASF:test_2_reheader\tN\tGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTATCTCTGCTGTGTGGTGGTGACCTTTGCACTGCCCGTGGGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCCGTCTCTGCTGTGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCCACAGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCCACAGGACGCCTGTCTCTGCTGTGTGGTGGTGACCTTTGCACTGCCCGTGGGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCTGTCTCTGCTGTGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCCGTCTCTGCTGCGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=600;END=903595;SUPPORT=6;COVERAGE=8,8,8,8,8;STRAND=+-;AF=0.75;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.5ASF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.3ESF|chr16;test_2_reheader_CHROM=Sniffles2.INS.5ASF|chr16;test_1_reheader_POS=Sniffles2.INS.3ESF|903595;test_2_reheader_POS=Sniffles2.INS.5ASF|903595;test_1_reheader_QUAL=Sniffles2.INS.3ESF|60;test_2_reheader_QUAL=Sniffles2.INS.5ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.3ESF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.5ASF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.3ESF|test_1|GT:0/1|GQ:3|DR:2|DV:6;test_2_reheader_SAMPLE=Sniffles2.INS.5ASF|test_2|GT:0/1|GQ:6|DR:5|DV:2;test_1_reheader_INFO=Sniffles2.INS.3ESF|PRECISE|SVTYPE:INS|SVLEN:600|END:903595|SUPPORT:6|COVERAGE:8:8:8:8:8|STRAND:+-|AF:0.75|STDEV_LEN:0.577|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.5ASF|IMPRECISE|SVTYPE:INS|SVLEN:600|END:903595|SUPPORT:2|COVERAGE:7:7:7:7:7|STRAND:+-|AF:0.286|STDEV_LEN:0.707|STDEV_POS:54.447|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:3:2:6\t0/1:6:5:2",
+                "chr16\t904025\tSniffles2.INS.5DSF\tN\tGCCCGCTGGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCTGTCTCTGCTGTGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCCGTCTCTGCTGCGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGGGCTACCTCCTCCCCGCGGCATCGCCCACAGGACGCCTGCGTCCCTGCTGCGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGTGGTGGCGACCTCTGCATCGCCACAGGACGCCTATCTCTGCTGTGTGGTGGTGACCTTTGCACTGCCCGTGGGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCTGTGGGGACGCCCGTCTCTGCTGTGTGGTGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGGGTGACCTCTGCATCGCCCACAGGACGCCTGTCTCTGCTGCGTGGTGGTGACCTCTGCACTGCCCACAGGACGCCTGTCTCTGCTGTGTGGTGGTGACCTCTGCACTGCCCACAGGACGCCTGTCTCTGCTGTGTGGTGGTGACCTTTGCATG\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=613;END=904025;SUPPORT=2;COVERAGE=7,7,7,7,7;STRAND=+-;AF=0.286;STDEV_LEN=7.071;STDEV_POS=25.456;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.5DSF|chr16;test_2_reheader_POS=Sniffles2.INS.5DSF|904025;test_2_reheader_QUAL=Sniffles2.INS.5DSF|60;test_2_reheader_FILTERS=Sniffles2.INS.5DSF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.5DSF|test_2|GT:0/1|GQ:6|DR:5|DV:2;test_2_reheader_INFO=Sniffles2.INS.5DSF|IMPRECISE|SVTYPE:INS|SVLEN:613|END:904025|SUPPORT:2|COVERAGE:7:7:7:7:7|STRAND:+-|AF:0.286|STDEV_LEN:7.071|STDEV_POS:25.456|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:6:5:2",
+                "chr16\t949510\tSniffles2.DEL.6ESF\taatgacagagtcagccaacgacagagtcagagccaacgacagagtcagagacaatgacagagtcagagacaacgacagagtcagagacgacagagtcagagacgacagagtcagagccaatgacagagtcagccaatgacagagtcagagccaacgacagagtcagccaatgacagagtcagagacaacgacagagtcagagacaacgacagagtcagagacgacagagtcagagacgacagagtcagagccaatgacagagtcagccaatgacagagtcagagccaacgacagagtcagccaatgacagagtcagagacaacgacagagttagagacaacgacagagtcagccaaggacagcgtcagccaacgacagaatcagagacaacgacagagtcagccaacgacagagtcagagccaatgagagtcagagccaacgacagagtcagagacgacagagtcagagccaacgacagagtcagccaacgacagagtcagagccaacgacagagtcagccaacgacagagtcagagccaacgacagagtcagccaacgacagagtcagagacaacgacagagtcagagccaacgacagagtcagagacgaaagactcagagccaatgacagagtcagagccaatgacagagtcagccaacgacagagtcagagccaacgacagagtcagccaatgacagagtcagagacagcgacagagttagagacaat\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-731;END=950241;SUPPORT=14;COVERAGE=22,22,22,23,22;STRAND=+-;AF=0.636;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.6ESF|chr16;test_1_reheader_POS=Sniffles2.DEL.6ESF|949510;test_1_reheader_QUAL=Sniffles2.DEL.6ESF|60;test_1_reheader_FILTERS=Sniffles2.DEL.6ESF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.6ESF|test_1|GT:0/1|GQ:40|DR:8|DV:14;test_1_reheader_INFO=Sniffles2.DEL.6ESF|PRECISE|SVTYPE:DEL|SVLEN:-731|END:950241|SUPPORT:14|COVERAGE:22:22:22:23:22|STRAND:+-|AF:0.636|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:40:8:14\t./.:.:.:.",
+                "chr16\t949565\tSniffles2.DEL.C0SF\tgacagagtcagagacaacgacagagtcagagacgacagagtcagagacgacagagtcagagccaatgacagagtcagccaatgacagagtcagagccaac\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-100;END=949665;SUPPORT=8;COVERAGE=31,30,32,32,32;STRAND=+-;AF=0.258;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.C0SF|chr16;test_2_reheader_POS=Sniffles2.DEL.C0SF|949565;test_2_reheader_QUAL=Sniffles2.DEL.C0SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.C0SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.C0SF|test_2|GT:0/1|GQ:15|DR:23|DV:8;test_2_reheader_INFO=Sniffles2.DEL.C0SF|PRECISE|SVTYPE:DEL|SVLEN:-100|END:949665|SUPPORT:8|COVERAGE:31:30:32:32:32|STRAND:+-|AF:0.258|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:15:23:8",
+                "chr16\t949708\tSniffles2.DEL.C3SF\tagagacaacgacagagtcagagacgacagagtcagagacgacagagtcagagccaatgacagagtcagccaatgacagagtcagagccaacgacagagtcagccaatgacagagtcagagacaacgacagagttagagacaacgacagagtcagccaaggacagcgtcagccaacgacagaatcagagacaacgacagagtcagccaacgacagagtcagagccaatgagagtcagagccaacgacagagtcagagacgacagagtcag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-269;END=949977;SUPPORT=8;COVERAGE=31,32,32,32,32;STRAND=+-;AF=0.25;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.C3SF|chr16;test_2_reheader_POS=Sniffles2.DEL.C3SF|949708;test_2_reheader_QUAL=Sniffles2.DEL.C3SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.C3SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.C3SF|test_2|GT:0/1|GQ:13|DR:24|DV:8;test_2_reheader_INFO=Sniffles2.DEL.C3SF|PRECISE|SVTYPE:DEL|SVLEN:-269|END:949977|SUPPORT:8|COVERAGE:31:32:32:32:32|STRAND:+-|AF:0.25|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:13:24:8",
+                "chr16\t950298\tSniffles2.DEL.C6SF\ttcagccaatgacagagtcagagacaacgacagagtcagccaacaacagtcagccaacgacagagtcaggccaacgacagagtcagccaatgacagagtcagagccaacgacagagtcagagacaacgacagagttagagacaacgacagagtc\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-153;END=950451;SUPPORT=10;COVERAGE=32,32,32,32,32;STRAND=+-;AF=0.312;STDEV_LEN=7.311;STDEV_POS=128.469;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.C6SF|chr16;test_2_reheader_POS=Sniffles2.DEL.C6SF|950298;test_2_reheader_QUAL=Sniffles2.DEL.C6SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.C6SF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.C6SF|test_2|GT:0/1|GQ:38|DR:22|DV:10;test_2_reheader_INFO=Sniffles2.DEL.C6SF|IMPRECISE|SVTYPE:DEL|SVLEN:-153|END:950451|SUPPORT:10|COVERAGE:32:32:32:32:32|STRAND:+-|AF:0.312|STDEV_LEN:7.311|STDEV_POS:128.469|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:38:22:10",
+                "chr16\t950488\tSniffles2.INS.40SF\tN\tCAACGACAGAGTCAGAGACAACGACAGAGTCAGAGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=36;END=950488;SUPPORT=14;COVERAGE=22,23,23,23,23;STRAND=+-;AF=0.609;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.INS.40SF|chr16;test_1_reheader_POS=Sniffles2.INS.40SF|950488;test_1_reheader_QUAL=Sniffles2.INS.40SF|60;test_1_reheader_FILTERS=Sniffles2.INS.40SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.40SF|test_1|GT:0/1|GQ:50|DR:9|DV:14;test_1_reheader_INFO=Sniffles2.INS.40SF|PRECISE|SVTYPE:INS|SVLEN:36|END:950488|SUPPORT:14|COVERAGE:22:23:23:23:23|STRAND:+-|AF:0.609|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:50:9:14\t./.:.:.:.",
+                "chr16\t952880\tSniffles2.DEL.71SF:test_1_reheader|Sniffles2.DEL.C8SF:test_2_reheader\ttccacacagacacccaccccaaaccagcctcctacacgtccacacagacacccaccccaaaccagcctcctgcacgtccacacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacacg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-178;END=953058;SUPPORT=16;COVERAGE=24,24,25,25,25;STRAND=+-;AF=0.64;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.C8SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.71SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.C8SF|chr16;test_1_reheader_POS=Sniffles2.DEL.71SF|952880;test_2_reheader_POS=Sniffles2.DEL.C8SF|952880;test_1_reheader_QUAL=Sniffles2.DEL.71SF|60;test_2_reheader_QUAL=Sniffles2.DEL.C8SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.71SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.C8SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.71SF|test_1|GT:0/1|GQ:45|DR:9|DV:16;test_2_reheader_SAMPLE=Sniffles2.DEL.C8SF|test_2|GT:0/1|GQ:41|DR:21|DV:10;test_1_reheader_INFO=Sniffles2.DEL.71SF|PRECISE|SVTYPE:DEL|SVLEN:-178|END:953058|SUPPORT:16|COVERAGE:24:24:25:25:25|STRAND:+-|AF:0.64|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.C8SF|PRECISE|SVTYPE:DEL|SVLEN:-178|END:953058|SUPPORT:10|COVERAGE:31:31:31:31:31|STRAND:+-|AF:0.323|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:45:9:16\t0/1:41:21:10",
+                "chr16\t953293\tSniffles2.DEL.72SF:test_1_reheader|Sniffles2.DEL.C9SF:test_2_reheader\tcaaaccagcctcctacacgtccacacagacacccaccccaaaccagcttcctacacgttcacacagacacgg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-72;END=953365;SUPPORT=15;COVERAGE=24,25,25,25,25;STRAND=+-;AF=0.6;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.C9SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.72SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.C9SF|chr16;test_1_reheader_POS=Sniffles2.DEL.72SF|953293;test_2_reheader_POS=Sniffles2.DEL.C9SF|953293;test_1_reheader_QUAL=Sniffles2.DEL.72SF|60;test_2_reheader_QUAL=Sniffles2.DEL.C9SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.72SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.C9SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.72SF|test_1|GT:0/1|GQ:58|DR:10|DV:15;test_2_reheader_SAMPLE=Sniffles2.DEL.C9SF|test_2|GT:0/1|GQ:41|DR:21|DV:10;test_1_reheader_INFO=Sniffles2.DEL.72SF|PRECISE|SVTYPE:DEL|SVLEN:-72|END:953365|SUPPORT:15|COVERAGE:24:25:25:25:25|STRAND:+-|AF:0.6|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.C9SF|PRECISE|SVTYPE:DEL|SVLEN:-72|END:953365|SUPPORT:10|COVERAGE:31:31:31:31:31|STRAND:+-|AF:0.323|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:58:10:15\t0/1:41:21:10",
+                "chr16\t953349\tSniffles2.DEL.75SF:test_1_reheader|Sniffles2.DEL.CDSF:test_2_reheader\tgttcacacagacacggaccccaaaccagcctcctacacgtccacacagacacccaccccaaaccagcctcctacacgttcacacagacacggaccccacaccagcctcctacacgtccacacagacacccaccccaaaccagcctcctgcacgtccacacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacacgtccacacagacacccactccaaaccagcctcctacacgtccacacagacaccccaaaccagcctcctacatgtccacacagacacccaccccaaaccagcctcctacatgtccacacagacacccaccccaaaccagcctcctacatgtccacacagacacccaccccaaaccagcctcctacat\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-440;END=953789;SUPPORT=9;COVERAGE=25,25,25,25,25;STRAND=+-;AF=0.36;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.CDSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.75SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.CDSF|chr16;test_1_reheader_POS=Sniffles2.DEL.75SF|953349;test_2_reheader_POS=Sniffles2.DEL.CDSF|953349;test_1_reheader_QUAL=Sniffles2.DEL.75SF|60;test_2_reheader_QUAL=Sniffles2.DEL.CDSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.75SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.CDSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.75SF|test_1|GT:0/1|GQ:45|DR:16|DV:9;test_2_reheader_SAMPLE=Sniffles2.DEL.CDSF|test_2|GT:0/1|GQ:60|DR:15|DV:16;test_1_reheader_INFO=Sniffles2.DEL.75SF|PRECISE|SVTYPE:DEL|SVLEN:-440|END:953789|SUPPORT:9|COVERAGE:25:25:25:25:25|STRAND:+-|AF:0.36|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.CDSF|PRECISE|SVTYPE:DEL|SVLEN:-440|END:953789|SUPPORT:16|COVERAGE:31:31:31:31:31|STRAND:+-|AF:0.516|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:45:16:9\t0/1:60:15:16",
+                "chr16\t953507\tSniffles2.DEL.73SF:test_1_reheader|Sniffles2.DEL.CBSF:test_2_reheader\tacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacatatccacacagacaccccaaaccagcctcctacacgtccacacag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-106;END=953613;SUPPORT=15;COVERAGE=25,25,25,25,25;STRAND=+-;AF=0.6;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.CBSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.73SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.CBSF|chr16;test_1_reheader_POS=Sniffles2.DEL.73SF|953507;test_2_reheader_POS=Sniffles2.DEL.CBSF|953507;test_1_reheader_QUAL=Sniffles2.DEL.73SF|60;test_2_reheader_QUAL=Sniffles2.DEL.CBSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.73SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.CBSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.73SF|test_1|GT:0/1|GQ:58|DR:10|DV:15;test_2_reheader_SAMPLE=Sniffles2.DEL.CBSF|test_2|GT:0/1|GQ:28|DR:22|DV:9;test_1_reheader_INFO=Sniffles2.DEL.73SF|PRECISE|SVTYPE:DEL|SVLEN:-106|END:953613|SUPPORT:15|COVERAGE:25:25:25:25:25|STRAND:+-|AF:0.6|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.CBSF|PRECISE|SVTYPE:DEL|SVLEN:-106|END:953613|SUPPORT:9|COVERAGE:31:31:31:31:31|STRAND:+-|AF:0.29|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:58:10:15\t0/1:28:22:9",
+                "chr16\t954972\tSniffles2.INS.41SF:test_1_reheader|Sniffles2.INS.60SF:test_2_reheader\tN\tCTAAGCGAACCAGACACGTTACATAAAATGCGTGCCTGCAGCAGACGGGGTCTGTGCACACACACACACAC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=71;END=954972;SUPPORT=13;COVERAGE=25,24,24,26,26;STRAND=+-;AF=0.542;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.60SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.41SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.60SF|chr16;test_1_reheader_POS=Sniffles2.INS.41SF|954972;test_2_reheader_POS=Sniffles2.INS.60SF|954972;test_1_reheader_QUAL=Sniffles2.INS.41SF|60;test_2_reheader_QUAL=Sniffles2.INS.60SF|60;test_1_reheader_FILTERS=Sniffles2.INS.41SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.60SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.41SF|test_1|GT:0/1|GQ:60|DR:11|DV:13;test_2_reheader_SAMPLE=Sniffles2.INS.60SF|test_2|GT:0/1|GQ:15|DR:23|DV:8;test_1_reheader_INFO=Sniffles2.INS.41SF|PRECISE|SVTYPE:INS|SVLEN:71|END:954972|SUPPORT:13|COVERAGE:25:24:24:26:26|STRAND:+-|AF:0.542|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.60SF|IMPRECISE|SVTYPE:INS|SVLEN:71|END:954972|SUPPORT:8|COVERAGE:32:31:31:32:33|STRAND:+-|AF:0.258|STDEV_LEN:2.345|STDEV_POS:27.353|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:11:13\t0/1:15:23:8",
+                "chr16\t955127\tSniffles2.INS.44SF:test_1_reheader|Sniffles2.INS.61SF:test_2_reheader\tN\tAACCAGACACGTTACATAAAATGCGTGCCTGCTGCAGACGTGGTGTGTGTATACACACACACACATCTAAGTAAACCAGACACGTTACATAAAATGCGTGCCCGCAGCAGACGTAGTGTGTGCATCCACACACACACATCTAAGTAAACTAGACACGTTACATAAAATGCGTGCCCACAGCAGACGCGGTGTGTGCGTACACACACACACATCTAAGTAAACTAGACACGTTACATAAAATGCGTGCCCGCAGCAGACGCAGTGTGTGCATACACATCTAAGTG\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=284;END=955127;SUPPORT=13;COVERAGE=27,26,26,26,27;STRAND=+-;AF=0.5;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.61SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.44SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.61SF|chr16;test_1_reheader_POS=Sniffles2.INS.44SF|955127;test_2_reheader_POS=Sniffles2.INS.61SF|955136;test_1_reheader_QUAL=Sniffles2.INS.44SF|60;test_2_reheader_QUAL=Sniffles2.INS.61SF|60;test_1_reheader_FILTERS=Sniffles2.INS.44SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.61SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.44SF|test_1|GT:0/1|GQ:60|DR:13|DV:13;test_2_reheader_SAMPLE=Sniffles2.INS.61SF|test_2|GT:0/1|GQ:48|DR:22|DV:11;test_1_reheader_INFO=Sniffles2.INS.44SF|PRECISE|SVTYPE:INS|SVLEN:284|END:955127|SUPPORT:13|COVERAGE:27:26:26:26:27|STRAND:+-|AF:0.5|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.61SF|IMPRECISE|SVTYPE:INS|SVLEN:286|END:955136|SUPPORT:11|COVERAGE:30:32:33:33:33|STRAND:+-|AF:0.333|STDEV_LEN:3.599|STDEV_POS:75.588|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:13:13\t0/1:48:22:11",
+                "chr16\t955473\tSniffles2.INS.45SF:test_1_reheader|Sniffles2.INS.64SF:test_2_reheader\tN\tACACACACACACACACATCTAAGTGAACCAGACACGTTACATAAAATGCGTGCCTGCAGCAGATGCGGTGTGTGCATACACACACACACATCTAAGTAAACCAGACACGTTACATAAAATGCGTGCCTGCAGCAGACGTAGTGTGTGCATCCACACACACACATCTAAGTAAACTAGACACGTTACATAAAATGCGTGCCCGCAGCAGAGACGGTGTGTGCGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=223;END=955473;SUPPORT=15;COVERAGE=24,26,26,27,27;STRAND=+-;AF=0.577;STDEV_LEN=0.5;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.64SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.45SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.64SF|chr16;test_1_reheader_POS=Sniffles2.INS.45SF|955473;test_2_reheader_POS=Sniffles2.INS.64SF|955473;test_1_reheader_QUAL=Sniffles2.INS.45SF|60;test_2_reheader_QUAL=Sniffles2.INS.64SF|60;test_1_reheader_FILTERS=Sniffles2.INS.45SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.64SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.45SF|test_1|GT:0/1|GQ:60|DR:11|DV:15;test_2_reheader_SAMPLE=Sniffles2.INS.64SF|test_2|GT:0/1|GQ:60|DR:21|DV:12;test_1_reheader_INFO=Sniffles2.INS.45SF|PRECISE|SVTYPE:INS|SVLEN:223|END:955473|SUPPORT:15|COVERAGE:24:26:26:27:27|STRAND:+-|AF:0.577|STDEV_LEN:0.5|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.64SF|PRECISE|SVTYPE:INS|SVLEN:223|END:955473|SUPPORT:12|COVERAGE:31:33:33:33:33|STRAND:+-|AF:0.364|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:11:15\t0/1:60:21:12",
+                "chr16\t955933\tSniffles2.INS.46SF:test_1_reheader|Sniffles2.INS.65SF:test_2_reheader\tN\tCACGGCACCCACCCCACGACGGCTCTCTCACATCCACAGGTCTCCGAGTTCACGTCC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=57;END=955933;SUPPORT=12;COVERAGE=26,27,27,29,29;STRAND=+-;AF=0.444;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.65SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.46SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.65SF|chr16;test_1_reheader_POS=Sniffles2.INS.46SF|955933;test_2_reheader_POS=Sniffles2.INS.65SF|955933;test_1_reheader_QUAL=Sniffles2.INS.46SF|60;test_2_reheader_QUAL=Sniffles2.INS.65SF|60;test_1_reheader_FILTERS=Sniffles2.INS.46SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.65SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.46SF|test_1|GT:0/1|GQ:60|DR:15|DV:12;test_2_reheader_SAMPLE=Sniffles2.INS.65SF|test_2|GT:0/1|GQ:60|DR:21|DV:12;test_1_reheader_INFO=Sniffles2.INS.46SF|PRECISE|SVTYPE:INS|SVLEN:57|END:955933|SUPPORT:12|COVERAGE:26:27:27:29:29|STRAND:+-|AF:0.444|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.65SF|IMPRECISE|SVTYPE:INS|SVLEN:57|END:955933|SUPPORT:12|COVERAGE:33:33:33:31:31|STRAND:+-|AF:0.364|STDEV_LEN:0.756|STDEV_POS:42.601|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:15:12\t0/1:60:21:12",
+                "chr16\t956173\tSniffles2.INS.47SF\tN\tCCCACGACGGCTCTCTCACATCCACAGGTCTCCGAGTTCACGTCTCACGGCGCCCA\t60\tGT\tPRECISE;SVTYPE=INS;SVLEN=57;END=956173;SUPPORT=5;COVERAGE=27,29,29,29,29;STRAND=+-;AF=0.172;STDEV_LEN=0.577;STDEV_POS=10.392;SUPPORT_LONG=0;FOUND_IN=sniffles;set=filterIntest_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.INS.47SF|chr16;test_1_reheader_POS=Sniffles2.INS.47SF|956173;test_1_reheader_QUAL=Sniffles2.INS.47SF|60;test_1_reheader_FILTERS=Sniffles2.INS.47SF|GT;test_1_reheader_SAMPLE=Sniffles2.INS.47SF|test_1|GT:0/0|GQ:16|DR:24|DV:5;test_1_reheader_INFO=Sniffles2.INS.47SF|PRECISE|SVTYPE:INS|SVLEN:57|END:956173|SUPPORT:5|COVERAGE:27:29:29:29:29|STRAND:+-|AF:0.172|STDEV_LEN:0.577|STDEV_POS:10.392|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/0:16:24:5\t./.:.:.:.",
+                "chr16\t960401\tSniffles2.DEL.7CSF:test_1_reheader|Sniffles2.DEL.D3SF:test_2_reheader\tacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacaacactggatcacaacccagacaccatctcatggtgacaacacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacaacacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacaacacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagac\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-864;END=961265;SUPPORT=13;COVERAGE=31,31,31,30,30;STRAND=+-;AF=0.419;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.DEL.D3SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.7CSF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.D3SF|chr16;test_1_reheader_POS=Sniffles2.DEL.7CSF|960401;test_2_reheader_POS=Sniffles2.DEL.D3SF|960552;test_1_reheader_QUAL=Sniffles2.DEL.7CSF|60;test_2_reheader_QUAL=Sniffles2.DEL.D3SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.7CSF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.D3SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.7CSF|test_1|GT:0/1|GQ:60|DR:18|DV:13;test_2_reheader_SAMPLE=Sniffles2.DEL.D3SF|test_2|GT:0/1|GQ:60|DR:16|DV:11;test_1_reheader_INFO=Sniffles2.DEL.7CSF|PRECISE|SVTYPE:DEL|SVLEN:-864|END:961265|SUPPORT:13|COVERAGE:31:31:31:30:30|STRAND:+-|AF:0.419|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.D3SF|IMPRECISE|SVTYPE:DEL|SVLEN:-713|END:961265|SUPPORT:11|COVERAGE:27:27:27:27:27|STRAND:+-|AF:0.407|STDEV_LEN:61.173|STDEV_POS:14.697|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:18:13\t0/1:60:16:11",
+                "chr16\t960535\tSniffles2.DEL.78SF:test_1_reheader|Sniffles2.DEL.D1SF:test_2_reheader\tcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacaacacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacagcacgggatcacgacccagacagactcacggtgacagcacgggatcacgacccagacacagactcacggtgacag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-262;END=960797;SUPPORT=14;COVERAGE=31,31,31,31,30;STRAND=+-;AF=0.452;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.DEL.D1SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.78SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.D1SF|chr16;test_1_reheader_POS=Sniffles2.DEL.78SF|960535;test_2_reheader_POS=Sniffles2.DEL.D1SF|960535;test_1_reheader_QUAL=Sniffles2.DEL.78SF|60;test_2_reheader_QUAL=Sniffles2.DEL.D1SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.78SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.D1SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.78SF|test_1|GT:0/1|GQ:60|DR:17|DV:14;test_2_reheader_SAMPLE=Sniffles2.DEL.D1SF|test_2|GT:0/1|GQ:60|DR:15|DV:12;test_1_reheader_INFO=Sniffles2.DEL.78SF|PRECISE|SVTYPE:DEL|SVLEN:-262|END:960797|SUPPORT:14|COVERAGE:31:31:31:31:30|STRAND:+-|AF:0.452|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.D1SF|IMPRECISE|SVTYPE:DEL|SVLEN:-262|END:960797|SUPPORT:12|COVERAGE:27:27:27:27:27|STRAND:+-|AF:0.444|STDEV_LEN:1.833|STDEV_POS:50.328|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:17:14\t0/1:60:15:12",
+                "chr16\t961793\tSniffles2.DEL.7ESF:test_1_reheader|Sniffles2.DEL.D4SF:test_2_reheader\tacagactcacggtgacagcacgggatcacgacccag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-36;END=961829;SUPPORT=13;COVERAGE=30,30,30,30,30;STRAND=+-;AF=0.433;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.D4SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.7ESF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.D4SF|chr16;test_1_reheader_POS=Sniffles2.DEL.7ESF|961793;test_2_reheader_POS=Sniffles2.DEL.D4SF|961793;test_1_reheader_QUAL=Sniffles2.DEL.7ESF|60;test_2_reheader_QUAL=Sniffles2.DEL.D4SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.7ESF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.D4SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.7ESF|test_1|GT:0/1|GQ:60|DR:17|DV:13;test_2_reheader_SAMPLE=Sniffles2.DEL.D4SF|test_2|GT:0/1|GQ:14|DR:20|DV:7;test_1_reheader_INFO=Sniffles2.DEL.7ESF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:961829|SUPPORT:13|COVERAGE:30:30:30:30:30|STRAND:+-|AF:0.433|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.D4SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:961829|SUPPORT:7|COVERAGE:27:27:27:27:27|STRAND:+-|AF:0.259|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:17:13\t0/1:14:20:7",
+                "chr16\t961981\tSniffles2.DEL.7FSF:test_1_reheader|Sniffles2.DEL.D5SF:test_2_reheader\tacagactcacggtgacagcacgggatcaccacccag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-36;END=962017;SUPPORT=12;COVERAGE=30,30,30,30,30;STRAND=+-;AF=0.4;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.D5SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.7FSF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.D5SF|chr16;test_1_reheader_POS=Sniffles2.DEL.7FSF|961981;test_2_reheader_POS=Sniffles2.DEL.D5SF|961981;test_1_reheader_QUAL=Sniffles2.DEL.7FSF|60;test_2_reheader_QUAL=Sniffles2.DEL.D5SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.7FSF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.D5SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.7FSF|test_1|GT:0/1|GQ:60|DR:18|DV:12;test_2_reheader_SAMPLE=Sniffles2.DEL.D5SF|test_2|GT:0/1|GQ:14|DR:20|DV:7;test_1_reheader_INFO=Sniffles2.DEL.7FSF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:962017|SUPPORT:12|COVERAGE:30:30:30:30:30|STRAND:+-|AF:0.4|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.D5SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:962017|SUPPORT:7|COVERAGE:27:27:27:27:26|STRAND:+-|AF:0.259|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:18:12\t0/1:14:20:7",
+                "chr16\t1040567\tSniffles2.INS.67SF\tN\tCCTGCCAAAGTCCCCACCGAGGTTCCCTCCGAGGTTCCCGCCGAGGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=47;END=1040567;SUPPORT=2;COVERAGE=2,2,2,2,2;STRAND=-;AF=1;STDEV_LEN=0.707;STDEV_POS=5.657;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.67SF|chr16;test_2_reheader_POS=Sniffles2.INS.67SF|1040567;test_2_reheader_QUAL=Sniffles2.INS.67SF|60;test_2_reheader_FILTERS=Sniffles2.INS.67SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.67SF|test_2|GT:1/1|GQ:5|DR:0|DV:2;test_2_reheader_INFO=Sniffles2.INS.67SF|PRECISE|SVTYPE:INS|SVLEN:47|END:1040567|SUPPORT:2|COVERAGE:2:2:2:2:2|STRAND:-|AF:1|STDEV_LEN:0.707|STDEV_POS:5.657|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:5:0:2",
+                "chr16\t1043243\tSniffles2.DEL.DBSF\tggtcagggacccctcgggtcagccttggggccgttctggggggtggtcagggacccctcgggtcagccttggggccgttccaggggggt\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-89;END=1043332;SUPPORT=4;COVERAGE=4,4,4,4,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.DBSF|chr16;test_2_reheader_POS=Sniffles2.DEL.DBSF|1043243;test_2_reheader_QUAL=Sniffles2.DEL.DBSF|60;test_2_reheader_FILTERS=Sniffles2.DEL.DBSF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.DBSF|test_2|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_INFO=Sniffles2.DEL.DBSF|PRECISE|SVTYPE:DEL|SVLEN:-89|END:1043332|SUPPORT:4|COVERAGE:4:4:4:4:5|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t1/1:11:0:4",
+                "chr16\t1075978\tSniffles2.INS.4ASF:test_1_reheader|Sniffles2.INS.6ASF:test_2_reheader\tN\tCCCTCCTCCCCTCCCCCTCCTTTCCCTCCCTCTCTCCCTCTCTCCTCCCCGCCTCCCCATCCCTCTCCCTCTCCCTCCTCTCTCTCTCCCCTACCCTGTCTTTCTCTCTGCCTCCCCGCCTCCCCTTCCCTCTCCCCATACCCTGTCTTTCTCTCTCCCT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=160;END=1075978;SUPPORT=5;COVERAGE=8,5,5,5,4;STRAND=+-;AF=1;STDEV_LEN=1.155;STDEV_POS=8.737;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.6ASF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.4ASF|chr16;test_2_reheader_CHROM=Sniffles2.INS.6ASF|chr16;test_1_reheader_POS=Sniffles2.INS.4ASF|1075978;test_2_reheader_POS=Sniffles2.INS.6ASF|1075983;test_1_reheader_QUAL=Sniffles2.INS.4ASF|60;test_2_reheader_QUAL=Sniffles2.INS.6ASF|60;test_1_reheader_FILTERS=Sniffles2.INS.4ASF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.6ASF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.4ASF|test_1|GT:1/1|GQ:13|DR:0|DV:5;test_2_reheader_SAMPLE=Sniffles2.INS.6ASF|test_2|GT:1/1|GQ:6|DR:3|DV:13;test_1_reheader_INFO=Sniffles2.INS.4ASF|PRECISE|SVTYPE:INS|SVLEN:160|END:1075978|SUPPORT:5|COVERAGE:8:5:5:5:4|STRAND:+-|AF:1|STDEV_LEN:1.155|STDEV_POS:8.737|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.6ASF|IMPRECISE|SVTYPE:INS|SVLEN:157|END:1075983|SUPPORT:13|COVERAGE:17:17:16:16:16|STRAND:+-|AF:0.812|STDEV_LEN:38.003|STDEV_POS:38.833|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:13:0:5\t1/1:6:3:13",
+                "chr16\t1076128\tSniffles2.DEL.84SF\tcctccccgcctccccatccctctccctctccctcctctctctctccccctaccctgttttctctctc\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-67;END=1076195;SUPPORT=2;COVERAGE=6,5,4,4,3;STRAND=+;AF=0.5;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.84SF|chr16;test_1_reheader_POS=Sniffles2.DEL.84SF|1076128;test_1_reheader_QUAL=Sniffles2.DEL.84SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.84SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.84SF|test_1|GT:0/1|GQ:14|DR:2|DV:2;test_1_reheader_INFO=Sniffles2.DEL.84SF|PRECISE|SVTYPE:DEL|SVLEN:-67|END:1076195|SUPPORT:2|COVERAGE:6:5:4:4:3|STRAND:+|AF:0.5|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:14:2:2\t./.:.:.:.",
+                "chr16\t1185669\tSniffles2.INS.6ESF\tN\tGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGTGTGGACGGGGCGGGTGAGTACGGTCGGCGTGCGCAGGGGCGGAGCGGGGTACGTGGGGGGCGGGTGAGAGACGGTCGGCATGCATAGGGCCGGGGGCGGGGTACGTGGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGTGGTGTGTAGACGGGGCGGGTGAGTAGACGGTCGGCGGGGTACGTGGGGGGCGGGTGAGGGCAGACGGTCGGCATGCATAGGGCCGGGGGCGGGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGTAGGCGCGCGCGGACGGGGCGGGTGAGTAGACGGTCGGTGCGGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTACGTGGGGGGCGGGTGAGAGGACGGCGTGCGTAGGGCGCAGGCGGTGTGCAGACGGGGCGGGTGAGTAGACGGTCGGCGTGCATAGGGGCCGAAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGCGTAGGGGCCAGGTAGACGGCGGTGCATAGGGGCCGGAGGGTGGGTGTGCACGGGCGGGCGAG\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=725;END=1185669;SUPPORT=3;COVERAGE=5,6,6,6,7;STRAND=+-;AF=0.5;STDEV_LEN=55.154;STDEV_POS=139.3;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.6ESF|chr16;test_2_reheader_POS=Sniffles2.INS.6ESF|1185669;test_2_reheader_QUAL=Sniffles2.INS.6ESF|60;test_2_reheader_FILTERS=Sniffles2.INS.6ESF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.6ESF|test_2|GT:0/1|GQ:21|DR:3|DV:3;test_2_reheader_INFO=Sniffles2.INS.6ESF|IMPRECISE|SVTYPE:INS|SVLEN:725|END:1185669|SUPPORT:3|COVERAGE:5:6:6:6:7|STRAND:+-|AF:0.5|STDEV_LEN:55.154|STDEV_POS:139.3|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:21:3:3",
+                "chr16\t1185837\tSniffles2.INS.6FSF\tN\tGGGTGCAGTGGGGGGCGGGTGAGTAGACGGCATGTGTAGGGGCAAGGGCAGGGGTGCGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCATAGGGGCCGGGGGCGGGGTGTGTACGGGGCGGGTGAATAGACGGTCGGCATGCATAGGGCCGGGGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGTGGTGTGTACGGGGCGGGTGAGTTAGACGGTCGGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGGATTGGGGCCGAAGGCAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCAGGTGAGTATAGACGGCGTGCATAGGGGCCGGAGGCGGGGTGTGTATGGGGCGGGTGAGTAGACGGTCGGCGTGCGTGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTCAGCGTGGGGCCGACGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCAGGTGAGTAGACGGCGTGCGTAGGGGCCGGAGGAGCGAGGTGGACGTGGGGGGCGGGTGAGTAGACGGCATGTGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTTGGGGCCGGAGGCGGGGTGTGTACGGGGCAGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCAGCGTGCGTAGGGGCCGGAGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCATAGGGGCCGGAGGCGGGGAGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCAGCGTGCGTAGGGGCCGGAGGCGGGCCGGGTACGTGGGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGTGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGGAGGCGGGGTACGTGGGGGGCGGGTGAGTAGACGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCATAGGGGCCGAAGGCGGGGTGTGTACGGGGCGCATGTAGACGGCGTAGGGGCCAGAGGCGGGGTGTGTACGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCAGGTGAGTAGACGGCGTGCATAGGGGCCGGAGGCGGGGTGTGTATGGGGCGGGTGAGTAGACGGTCGGCGTGCGTAGGGGCCGGAGGCGGGGTGTGTACGGGGCGGGTGAGTACGCGTGGGGACGGGCGTGTGGGCGGGTGGGTGGGGAGGGGTGGGCGGGCCGGGGCGCTCGGGGCAGGTGGGTGGCGGGGTGGCGCGT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=1414;END=1185837;SUPPORT=5;COVERAGE=6,6,7,7,7;STRAND=+-;AF=0.714;STDEV_LEN=153.895;STDEV_POS=111.482;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.6FSF|chr16;test_2_reheader_POS=Sniffles2.INS.6FSF|1185837;test_2_reheader_QUAL=Sniffles2.INS.6FSF|60;test_2_reheader_FILTERS=Sniffles2.INS.6FSF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.6FSF|test_2|GT:0/1|GQ:6|DR:2|DV:5;test_2_reheader_INFO=Sniffles2.INS.6FSF|IMPRECISE|SVTYPE:INS|SVLEN:1414|END:1185837|SUPPORT:5|COVERAGE:6:6:7:7:7|STRAND:+-|AF:0.714|STDEV_LEN:153.895|STDEV_POS:111.482|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:6:2:5",
+                "chr16\t1190923\tSniffles2.INS.4ESF:test_1_reheader|Sniffles2.INS.70SF:test_2_reheader\tN\tGGGTTTCGCTGACCCAGCAGGCTGGCCTGGTTGTGTGGCCTCAGGCACACTCGGGGTTTCGGTGACCCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCGGGGTCTCTCTGACTCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCGGGGTCTCTCTGACTCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCGGGGTCTCTCTTACTCAGCAGGCTGGCCTGGCTGTGTGGCCTCCGGCACACTCGGGGTCTCTGACCCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCGGGGTTTCGGTGACCCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCAGGGTTTTGGTGACCCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTTGGGGTCTCTGACCCAGTAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTCGGGGTCTCTGACCCAGCAGGCTGGCCTGGCTGTGTGGCCTCAGGCACACTC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=523;END=1190923;SUPPORT=3;COVERAGE=10,10,10,10,11;STRAND=+;AF=0.3;STDEV_LEN=2.646;STDEV_POS=50.013;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.70SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.4ESF|chr16;test_2_reheader_CHROM=Sniffles2.INS.70SF|chr16;test_1_reheader_POS=Sniffles2.INS.4ESF|1190923;test_2_reheader_POS=Sniffles2.INS.70SF|1190943;test_1_reheader_QUAL=Sniffles2.INS.4ESF|60;test_2_reheader_QUAL=Sniffles2.INS.70SF|60;test_1_reheader_FILTERS=Sniffles2.INS.4ESF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.70SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.4ESF|test_1|GT:0/1|GQ:10|DR:7|DV:3;test_2_reheader_SAMPLE=Sniffles2.INS.70SF|test_2|GT:0/1|GQ:36|DR:5|DV:5;test_1_reheader_INFO=Sniffles2.INS.4ESF|IMPRECISE|SVTYPE:INS|SVLEN:523|END:1190923|SUPPORT:3|COVERAGE:10:10:10:10:11|STRAND:+|AF:0.3|STDEV_LEN:2.646|STDEV_POS:50.013|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.70SF|IMPRECISE|SVTYPE:INS|SVLEN:524|END:1190943|SUPPORT:5|COVERAGE:9:10:10:10:10|STRAND:+-|AF:0.5|STDEV_LEN:2.887|STDEV_POS:35.907|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:10:7:3\t0/1:36:5:5",
+                "chr16\t1191001\tSniffles2.DEL.86SF\tcctggctgtgtggcctcaggcacactcggggtctctgacccagcaggctggcctggctgtgtggcctcaggcacactcggggtctctctgactcagcaggctggcctggctgtgtggcctcaggcacactcggggtctctctgactcagcaggctggcctggctgtgtggcctcaggcacactcggggtctctcttactcagcaggctgg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-210;END=1191211;SUPPORT=7;COVERAGE=10,10,11,11,11;STRAND=+-;AF=0.636;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.86SF|chr16;test_1_reheader_POS=Sniffles2.DEL.86SF|1191001;test_1_reheader_QUAL=Sniffles2.DEL.86SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.86SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.86SF|test_1|GT:0/1|GQ:20|DR:4|DV:7;test_1_reheader_INFO=Sniffles2.DEL.86SF|PRECISE|SVTYPE:DEL|SVLEN:-210|END:1191211|SUPPORT:7|COVERAGE:10:10:11:11:11|STRAND:+-|AF:0.636|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:20:4:7\t./.:.:.:.",
+                "chr16\t1191090\tSniffles2.DEL.DESF\tgactcagcaggctggcctggctgtgtggcctcaggcacactcggggtctctctgactcagcaggctggcctggctgtgtggcctcaggcacactcggggtctctcttactcagcaggctggcctggctgtgtggcctcaggcacactcggggtctctgacccagcaggctggcctggctgtgtggcctcaggcacactcggggtctctct\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-210;END=1191300;SUPPORT=3;COVERAGE=9,10,10,10,10;STRAND=+-;AF=0.3;STDEV_LEN=0.577;STDEV_POS=51.384;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.DESF|chr16;test_2_reheader_POS=Sniffles2.DEL.DESF|1191090;test_2_reheader_QUAL=Sniffles2.DEL.DESF|60;test_2_reheader_FILTERS=Sniffles2.DEL.DESF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.DESF|test_2|GT:0/1|GQ:10|DR:7|DV:3;test_2_reheader_INFO=Sniffles2.DEL.DESF|IMPRECISE|SVTYPE:DEL|SVLEN:-210|END:1191300|SUPPORT:3|COVERAGE:9:10:10:10:10|STRAND:+-|AF:0.3|STDEV_LEN:0.577|STDEV_POS:51.384|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:10:7:3",
+                "chr16\t1204953\tSniffles2.INS.50SF:test_1_reheader|Sniffles2.INS.4FSF:test_1_reheader|Sniffles2.INS.74SF:test_2_reheader|Sniffles2.INS.73SF:test_2_reheader\tN\tGGGCCCCAGATCAGTGCCGGGGAGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGGCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGGCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGTGGGGCCCCAGATCAGTGCCGGGGAGGGGTGGGAGCCGCGGGT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=418;END=1204953;SUPPORT=8;COVERAGE=17,16,15,15,15;STRAND=+-;AF=0.533;STDEV_LEN=0.816;STDEV_POS=64;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.4FSF:test_1_reheader|Sniffles2.INS.74SF:test_2_reheader|Sniffles2.INS.73SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.50SF|chr16,Sniffles2.INS.4FSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.74SF|chr16,Sniffles2.INS.73SF|chr16;test_1_reheader_POS=Sniffles2.INS.50SF|1204953,Sniffles2.INS.4FSF|1204961;test_2_reheader_POS=Sniffles2.INS.74SF|1204953,Sniffles2.INS.73SF|1204971;test_1_reheader_QUAL=Sniffles2.INS.50SF|60,Sniffles2.INS.4FSF|60;test_2_reheader_QUAL=Sniffles2.INS.74SF|60,Sniffles2.INS.73SF|60;test_1_reheader_FILTERS=Sniffles2.INS.50SF|PASS,Sniffles2.INS.4FSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.74SF|PASS,Sniffles2.INS.73SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.50SF|test_1|GT:0/1|GQ:47|DR:7|DV:8,Sniffles2.INS.4FSF|test_1|GT:0/1|GQ:47|DR:7|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.74SF|test_2|GT:0/1|GQ:32|DR:6|DV:10,Sniffles2.INS.73SF|test_2|GT:0/1|GQ:6|DR:12|DV:4;test_1_reheader_INFO=Sniffles2.INS.50SF|IMPRECISE|SVTYPE:INS|SVLEN:418|END:1204953|SUPPORT:8|COVERAGE:17:16:15:15:15|STRAND:+-|AF:0.533|STDEV_LEN:0.816|STDEV_POS:64|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.4FSF|IMPRECISE|SVTYPE:INS|SVLEN:209|END:1204961|SUPPORT:8|COVERAGE:17:16:15:15:15|STRAND:+-|AF:0.533|STDEV_LEN:0.577|STDEV_POS:91.065|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.74SF|IMPRECISE|SVTYPE:INS|SVLEN:417|END:1204953|SUPPORT:10|COVERAGE:17:16:16:16:16|STRAND:+-|AF:0.625|STDEV_LEN:5.563|STDEV_POS:20.004|SUPPORT_LONG:0|FOUND_IN:sniffles,Sniffles2.INS.73SF|IMPRECISE|SVTYPE:INS|SVLEN:210|END:1204971|SUPPORT:4|COVERAGE:17:16:16:16:16|STRAND:+-|AF:0.25|STDEV_LEN:0|STDEV_POS:72.125|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:47:7:8\t0/1:6:12:4",
+                "chr16\t1230996\tSniffles2.DEL.E1SF\tccccagcccagctccccatggactcacccccagccccagcccagctccccatggactcacccccagccccagcccagctgcccatggactagtcccagccccagccccagctccccatggactcacccccagccccagcccagctccccatggactcacccccagccccagcccagctccccatggactagtcgcagcccccggccccagctccccatggtctcacccccag\tN\t60\tGT\tPRECISE;SVTYPE=DEL;SVLEN=-232;END=1231228;SUPPORT=2;COVERAGE=13,13,13,13,13;STRAND=-;AF=0.154;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.E1SF|chr16;test_2_reheader_POS=Sniffles2.DEL.E1SF|1230996;test_2_reheader_QUAL=Sniffles2.DEL.E1SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.E1SF|GT;test_2_reheader_SAMPLE=Sniffles2.DEL.E1SF|test_2|GT:0/0|GQ:10|DR:11|DV:2;test_2_reheader_INFO=Sniffles2.DEL.E1SF|PRECISE|SVTYPE:DEL|SVLEN:-232|END:1231228|SUPPORT:2|COVERAGE:13:13:13:13:13|STRAND:-|AF:0.154|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:10:11:2",
+                "chr16\t1231234\tSniffles2.INS.52SF:test_1_reheader|Sniffles2.INS.76SF:test_2_reheader\tN\tCCCAGCTCCCCATGGACTAGTCCCAGCCCCAGCCCAGCTCCCCATGGTCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTAGTCCCATCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCTCCA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=132;END=1231234;SUPPORT=4;COVERAGE=14,14,14,14,14;STRAND=-;AF=0.286;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.INS.76SF:test_2_reheader;set=test_1_reheader-filterIntest_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.52SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.76SF|chr16;test_1_reheader_POS=Sniffles2.INS.52SF|1231234;test_2_reheader_POS=Sniffles2.INS.76SF|1231235;test_1_reheader_QUAL=Sniffles2.INS.52SF|60;test_2_reheader_QUAL=Sniffles2.INS.76SF|60;test_1_reheader_FILTERS=Sniffles2.INS.52SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.76SF|GT;test_1_reheader_SAMPLE=Sniffles2.INS.52SF|test_1|GT:0/1|GQ:12|DR:10|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.76SF|test_2|GT:0/0|GQ:10|DR:11|DV:2;test_1_reheader_INFO=Sniffles2.INS.52SF|PRECISE|SVTYPE:INS|SVLEN:132|END:1231234|SUPPORT:4|COVERAGE:14:14:14:14:14|STRAND:-|AF:0.286|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.76SF|IMPRECISE|SVTYPE:INS|SVLEN:135|END:1231235|SUPPORT:2|COVERAGE:13:13:13:13:13|STRAND:-|AF:0.154|STDEV_LEN:2.121|STDEV_POS:29.698|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:12:10:4\t0/0:10:11:2",
+                "chr16\t1231287\tSniffles2.DEL.E2SF\tcccccagccccagcccagctccccatggactagtcccatcccccggccccagctccccatggtctcacccccagccccagcccagctccccatggtctcacccccagccccagcccagctccccatggactcacccccagccccagcccagctccccatggactagtcccagcccccggccccagctccccatggtctcacccccagccccagcccagctccccatggtctcacccccggccccagctccctgtggacttg\tN\t60\tGT\tPRECISE;SVTYPE=DEL;SVLEN=-261;END=1231548;SUPPORT=2;COVERAGE=13,13,13,13,13;STRAND=-;AF=0.154;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.E2SF|chr16;test_2_reheader_POS=Sniffles2.DEL.E2SF|1231287;test_2_reheader_QUAL=Sniffles2.DEL.E2SF|60;test_2_reheader_FILTERS=Sniffles2.DEL.E2SF|GT;test_2_reheader_SAMPLE=Sniffles2.DEL.E2SF|test_2|GT:0/0|GQ:10|DR:11|DV:2;test_2_reheader_INFO=Sniffles2.DEL.E2SF|PRECISE|SVTYPE:DEL|SVLEN:-261|END:1231548|SUPPORT:2|COVERAGE:13:13:13:13:13|STRAND:-|AF:0.154|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:10:11:2",
+                "chr16\t1231356\tSniffles2.INS.78SF\tN\tCCCAGCTCCAGCCCAGCTCCCCATGGACTAGTCCCAGCCCCAGCCCAGCTCCCCATGGTCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTAGTCCCATCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGTCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTAGTCGCAGCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCTCCCCATGGACTAGTCTAGTCCCAGCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCTCCAGCCCAGCTCCCCATGGACTAGTCCCAGCCCCAGCCCAGCTCCCCATGGT\t60\tGT\tIMPRECISE;SVTYPE=INS;SVLEN=385;END=1231356;SUPPORT=2;COVERAGE=13,13,13,13,13;STRAND=+-;AF=0.154;STDEV_LEN=7.778;STDEV_POS=24.749;SUPPORT_LONG=0;FOUND_IN=sniffles;set=filterIntest_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.78SF|chr16;test_2_reheader_POS=Sniffles2.INS.78SF|1231356;test_2_reheader_QUAL=Sniffles2.INS.78SF|60;test_2_reheader_FILTERS=Sniffles2.INS.78SF|GT;test_2_reheader_SAMPLE=Sniffles2.INS.78SF|test_2|GT:0/0|GQ:10|DR:11|DV:2;test_2_reheader_INFO=Sniffles2.INS.78SF|IMPRECISE|SVTYPE:INS|SVLEN:385|END:1231356|SUPPORT:2|COVERAGE:13:13:13:13:13|STRAND:+-|AF:0.154|STDEV_LEN:7.778|STDEV_POS:24.749|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/0:10:11:2",
+                "chr16\t1231416\tSniffles2.INS.53SF:test_1_reheader|Sniffles2.INS.77SF:test_2_reheader\tN\tCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTAGTCGCAGCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCTCCCCATGGACTAGTCCCAGCCCCAGCCCAGCTCCCCATGGTCTCACCCCCAGCCCCAGCCCAGCTCCCCATGGACTAGTCCCAGCCCCCGGCCCCAGCTCCCCATGGTCTCACCCCCAGCTCCAGCCCAGCTCCCCATGGACTAGTCCCAGCCCCAGCCCAGCTCCCCATGGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=252;END=1231416;SUPPORT=4;COVERAGE=14,14,14,14,13;STRAND=-;AF=0.286;STDEV_LEN=0.707;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.77SF:test_2_reheader;set=test_1_reheader-filterIntest_2_reheader;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.53SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.77SF|chr16;test_1_reheader_POS=Sniffles2.INS.53SF|1231416;test_2_reheader_POS=Sniffles2.INS.77SF|1231446;test_1_reheader_QUAL=Sniffles2.INS.53SF|60;test_2_reheader_QUAL=Sniffles2.INS.77SF|60;test_1_reheader_FILTERS=Sniffles2.INS.53SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.77SF|GT;test_1_reheader_SAMPLE=Sniffles2.INS.53SF|test_1|GT:0/1|GQ:12|DR:10|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.77SF|test_2|GT:0/0|GQ:10|DR:11|DV:2;test_1_reheader_INFO=Sniffles2.INS.53SF|PRECISE|SVTYPE:INS|SVLEN:252|END:1231416|SUPPORT:4|COVERAGE:14:14:14:14:13|STRAND:-|AF:0.286|STDEV_LEN:0.707|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.77SF|PRECISE|SVTYPE:INS|SVLEN:256|END:1231446|SUPPORT:2|COVERAGE:13:13:13:13:13|STRAND:-|AF:0.154|STDEV_LEN:2.121|STDEV_POS:21.213|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:12:10:4\t0/0:10:11:2",
+                "chr16\t1238068\tSniffles2.INS.79SF\tN\tGTGTGTGAATGTGTGCATGTGTTCGTGTGTGCATGTGAACATCCGTGTGTGCATATGTGCATGTGAGTGCACAGATGTGCGGTGTGTGTGCA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=92;END=1238068;SUPPORT=3;COVERAGE=8,8,8,8,2;STRAND=+-;AF=0.375;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.79SF|chr16;test_2_reheader_POS=Sniffles2.INS.79SF|1238068;test_2_reheader_QUAL=Sniffles2.INS.79SF|60;test_2_reheader_FILTERS=Sniffles2.INS.79SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.79SF|test_2|GT:0/1|GQ:16|DR:5|DV:3;test_2_reheader_INFO=Sniffles2.INS.79SF|PRECISE|SVTYPE:INS|SVLEN:92|END:1238068|SUPPORT:3|COVERAGE:8:8:8:8:2|STRAND:+-|AF:0.375|STDEV_LEN:0.577|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:16:5:3",
+                "chr16\t1238210\tSniffles2.INS.7ASF\tN\tGTGCATATGTGTGCGTGTGTGCACACACGTGTGTACATGTGTGA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=44;END=1238210;SUPPORT=6;COVERAGE=8,8,8,8,2;STRAND=+-;AF=0.75;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.7ASF|chr16;test_2_reheader_POS=Sniffles2.INS.7ASF|1238210;test_2_reheader_QUAL=Sniffles2.INS.7ASF|60;test_2_reheader_FILTERS=Sniffles2.INS.7ASF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.7ASF|test_2|GT:0/1|GQ:3|DR:2|DV:6;test_2_reheader_INFO=Sniffles2.INS.7ASF|PRECISE|SVTYPE:INS|SVLEN:44|END:1238210|SUPPORT:6|COVERAGE:8:8:8:8:2|STRAND:+-|AF:0.75|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:3:2:6",
+                "chr16\t1248124\tSniffles2.DEL.8CSF:test_1_reheader|Sniffles2.DEL.ECSF:test_2_reheader\tcactcacacatgtacacatgtgtgtgcacacacgcacacatatg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-44;END=1248168;SUPPORT=4;COVERAGE=1,4,4,4,5;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.ECSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.8CSF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.ECSF|chr16;test_1_reheader_POS=Sniffles2.DEL.8CSF|1248124;test_2_reheader_POS=Sniffles2.DEL.ECSF|1248124;test_1_reheader_QUAL=Sniffles2.DEL.8CSF|60;test_2_reheader_QUAL=Sniffles2.DEL.ECSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.8CSF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.ECSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.8CSF|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.DEL.ECSF|test_2|GT:1/1|GQ:11|DR:0|DV:4;test_1_reheader_INFO=Sniffles2.DEL.8CSF|PRECISE|SVTYPE:DEL|SVLEN:-44|END:1248168|SUPPORT:4|COVERAGE:1:4:4:4:5|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.ECSF|PRECISE|SVTYPE:DEL|SVLEN:-44|END:1248168|SUPPORT:4|COVERAGE:2:4:4:4:4|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t1/1:11:0:4",
+                "chr16\t1248322\tSniffles2.DEL.8DSF:test_1_reheader|Sniffles2.DEL.EDSF:test_2_reheader\tgcacatatgcacacacggatgttcacatgcacacacgaacacatgcacacattcacaca\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-59;END=1248381;SUPPORT=4;COVERAGE=4,4,4,4,6;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.EDSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.8DSF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.EDSF|chr16;test_1_reheader_POS=Sniffles2.DEL.8DSF|1248322;test_2_reheader_POS=Sniffles2.DEL.EDSF|1248302;test_1_reheader_QUAL=Sniffles2.DEL.8DSF|60;test_2_reheader_QUAL=Sniffles2.DEL.EDSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.8DSF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.EDSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.8DSF|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.DEL.EDSF|test_2|GT:1/1|GQ:11|DR:0|DV:4;test_1_reheader_INFO=Sniffles2.DEL.8DSF|PRECISE|SVTYPE:DEL|SVLEN:-59|END:1248381|SUPPORT:4|COVERAGE:4:4:4:4:6|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.EDSF|PRECISE|SVTYPE:DEL|SVLEN:-59|END:1248361|SUPPORT:4|COVERAGE:3:4:4:4:4|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t1/1:11:0:4",
+                "chr16\t1254908\tSniffles2.DEL.8ESF:test_1_reheader|Sniffles2.DEL.EESF:test_2_reheader\tccatggggagctggggccgggggctgggactagtccatggggagctgggctggggctgggggtgaga\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-67;END=1254975;SUPPORT=8;COVERAGE=14,14,14,14,14;STRAND=+-;AF=0.571;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.EESF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.8ESF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.EESF|chr16;test_1_reheader_POS=Sniffles2.DEL.8ESF|1254908;test_2_reheader_POS=Sniffles2.DEL.EESF|1254909;test_1_reheader_QUAL=Sniffles2.DEL.8ESF|60;test_2_reheader_QUAL=Sniffles2.DEL.EESF|60;test_1_reheader_FILTERS=Sniffles2.DEL.8ESF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.EESF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.8ESF|test_1|GT:0/1|GQ:37|DR:6|DV:8;test_2_reheader_SAMPLE=Sniffles2.DEL.EESF|test_2|GT:0/1|GQ:11|DR:3|DV:2;test_1_reheader_INFO=Sniffles2.DEL.8ESF|PRECISE|SVTYPE:DEL|SVLEN:-67|END:1254975|SUPPORT:8|COVERAGE:14:14:14:14:14|STRAND:+-|AF:0.571|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.EESF|PRECISE|SVTYPE:DEL|SVLEN:-66|END:1254975|SUPPORT:2|COVERAGE:5:5:5:5:7|STRAND:-|AF:0.4|STDEV_LEN:0.707|STDEV_POS:11.314|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:37:6:8\t0/1:11:3:2",
+                "chr16\t1254975\tSniffles2.INS.57SF:test_1_reheader|Sniffles2.INS.7CSF:test_2_reheader\tN\tCCATGGGGAGCTGGGCTGGGGCTGGGACTAGTCCATGGGGAGCTGGGCTGGGGCTGGGACTAGTTCATGGGGAGCTGGGCTGGGGCTGGGACTAGTTCATGGGAGCTGGGCTGGGGCTGGGACTAGTCCATGGGGAGCTGGGCTGGGGCTGGGACTAGTTCATGGGGAGCTGGGCTGGGGCTGGGGGTGAGTCCATGGGGAGCTGGGCTGGGGCTGGGGGTGAGT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=225;END=1254975;SUPPORT=6;COVERAGE=14,14,14,14,14;STRAND=+-;AF=0.429;STDEV_LEN=0.577;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.7CSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.57SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.7CSF|chr16;test_1_reheader_POS=Sniffles2.INS.57SF|1254975;test_2_reheader_POS=Sniffles2.INS.7CSF|1254975;test_1_reheader_QUAL=Sniffles2.INS.57SF|60;test_2_reheader_QUAL=Sniffles2.INS.7CSF|60;test_1_reheader_FILTERS=Sniffles2.INS.57SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.7CSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.57SF|test_1|GT:0/1|GQ:37|DR:8|DV:6;test_2_reheader_SAMPLE=Sniffles2.INS.7CSF|test_2|GT:0/1|GQ:11|DR:3|DV:2;test_1_reheader_INFO=Sniffles2.INS.57SF|PRECISE|SVTYPE:INS|SVLEN:225|END:1254975|SUPPORT:6|COVERAGE:14:14:14:14:14|STRAND:+-|AF:0.429|STDEV_LEN:0.577|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.7CSF|PRECISE|SVTYPE:INS|SVLEN:226|END:1254975|SUPPORT:2|COVERAGE:5:5:5:5:7|STRAND:+-|AF:0.4|STDEV_LEN:0.707|STDEV_POS:21.92|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:37:8:6\t0/1:11:3:2",
+                "chr16\t1258684\tSniffles2.INS.58SF:test_1_reheader|Sniffles2.INS.7ESF:test_2_reheader\tN\tTGAGCCCCCTCCCCCACCCTGAGCCCCCTCCCCTGTCTTGAGCCCCTGCTCCATCCTGAGTCCCCTCCCCCACACTGAGCCCCCTCCCCTTTCTTGAGCCCCTCATCCATCCTGAGCCCCTCCTCCATCCTGAGCCCCCTCCCCCATCCTGGGCCCCCTCCCCTTTCTTGAGCCCCCCTCCCCCACCCTGAGCCCCCTCCCCTTTCTTGAGCCCCCTCCCCCACCTGAGCCCCTTCCCCTTTCTTGAGTCCCTCCTCCATCCTGAGCCCCCTCCCCTTTCTTGAGCCCCTCCTCCACCCTCAGCCCCCTCCCCTTTCTTGAGCCCCTCCTCCACCCTCAGCCCCCTCCCCTTTCT\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=355;END=1258684;SUPPORT=14;COVERAGE=14,14,14,14,14;STRAND=+-;AF=1;STDEV_LEN=37.175;STDEV_POS=1.69;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.7ESF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.58SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.7ESF|chr16;test_1_reheader_POS=Sniffles2.INS.58SF|1258684;test_2_reheader_POS=Sniffles2.INS.7ESF|1258685;test_1_reheader_QUAL=Sniffles2.INS.58SF|60;test_2_reheader_QUAL=Sniffles2.INS.7ESF|60;test_1_reheader_FILTERS=Sniffles2.INS.58SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.7ESF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.58SF|test_1|GT:1/1|GQ:39|DR:0|DV:14;test_2_reheader_SAMPLE=Sniffles2.INS.7ESF|test_2|GT:1/1|GQ:30|DR:0|DV:11;test_1_reheader_INFO=Sniffles2.INS.58SF|IMPRECISE|SVTYPE:INS|SVLEN:355|END:1258684|SUPPORT:14|COVERAGE:14:14:14:14:14|STRAND:+-|AF:1|STDEV_LEN:37.175|STDEV_POS:1.69|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.7ESF|IMPRECISE|SVTYPE:INS|SVLEN:424|END:1258685|SUPPORT:11|COVERAGE:9:11:11:11:15|STRAND:+-|AF:1|STDEV_LEN:34.141|STDEV_POS:1.89|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:39:0:14\t1/1:30:0:11",
+                "chr16\t1260690\tSniffles2.INS.59SF:test_1_reheader|Sniffles2.INS.7FSF:test_2_reheader\tN\tAGCCCGGAGACCCACGTCCACACACAGCCCGGAGACCCACATCCACACAC\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=50;END=1260690;SUPPORT=7;COVERAGE=15,15,15,16,16;STRAND=+-;AF=0.467;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.7FSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.59SF|chr16;test_2_reheader_CHROM=Sniffles2.INS.7FSF|chr16;test_1_reheader_POS=Sniffles2.INS.59SF|1260690;test_2_reheader_POS=Sniffles2.INS.7FSF|1260690;test_1_reheader_QUAL=Sniffles2.INS.59SF|60;test_2_reheader_QUAL=Sniffles2.INS.7FSF|60;test_1_reheader_FILTERS=Sniffles2.INS.59SF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.7FSF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.59SF|test_1|GT:0/1|GQ:47|DR:8|DV:7;test_2_reheader_SAMPLE=Sniffles2.INS.7FSF|test_2|GT:0/1|GQ:54|DR:9|DV:8;test_1_reheader_INFO=Sniffles2.INS.59SF|PRECISE|SVTYPE:INS|SVLEN:50|END:1260690|SUPPORT:7|COVERAGE:15:15:15:16:16|STRAND:+-|AF:0.467|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.7FSF|PRECISE|SVTYPE:INS|SVLEN:50|END:1260690|SUPPORT:8|COVERAGE:17:17:17:17:16|STRAND:+-|AF:0.471|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:47:8:7\t0/1:54:9:8",
+                "chr16\t1264730\tSniffles2.DEL.90SF:test_1_reheader|Sniffles2.DEL.EFSF:test_2_reheader\ttgtgtgtatgcgtgtgcatatgtaaggatgtgtgcg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-36;END=1264766;SUPPORT=6;COVERAGE=15,15,13,12,12;STRAND=+-;AF=0.462;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.EFSF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.90SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.EFSF|chr16;test_1_reheader_POS=Sniffles2.DEL.90SF|1264730;test_2_reheader_POS=Sniffles2.DEL.EFSF|1264730;test_1_reheader_QUAL=Sniffles2.DEL.90SF|60;test_2_reheader_QUAL=Sniffles2.DEL.EFSF|60;test_1_reheader_FILTERS=Sniffles2.DEL.90SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.EFSF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.90SF|test_1|GT:0/1|GQ:40|DR:7|DV:6;test_2_reheader_SAMPLE=Sniffles2.DEL.EFSF|test_2|GT:0/1|GQ:37|DR:6|DV:8;test_1_reheader_INFO=Sniffles2.DEL.90SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:1264766|SUPPORT:6|COVERAGE:15:15:13:12:12|STRAND:+-|AF:0.462|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.EFSF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:1264766|SUPPORT:8|COVERAGE:14:14:14:14:14|STRAND:+-|AF:0.571|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:40:7:6\t0/1:37:6:8",
+                "chr16\t1285139\tSniffles2.INS.80SF\tN\tACTCTCCACTATTCCAGGGCCTCATCCCACTCCAGGGCCCTCTCACTATTCCAGGGCCCTCTCCCCCCA\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=80;END=1285139;SUPPORT=3;COVERAGE=4,4,4,4,4;STRAND=+-;AF=0.75;STDEV_LEN=12.53;STDEV_POS=50.013;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.80SF|chr16;test_2_reheader_POS=Sniffles2.INS.80SF|1285139;test_2_reheader_QUAL=Sniffles2.INS.80SF|60;test_2_reheader_FILTERS=Sniffles2.INS.80SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.80SF|test_2|GT:0/1|GQ:1|DR:1|DV:3;test_2_reheader_INFO=Sniffles2.INS.80SF|IMPRECISE|SVTYPE:INS|SVLEN:80|END:1285139|SUPPORT:3|COVERAGE:4:4:4:4:4|STRAND:+-|AF:0.75|STDEV_LEN:12.53|STDEV_POS:50.013|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:1:1:3",
+                "chr16\t1285239\tSniffles2.INS.81SF\tN\tCCAGGGCCCTCTCCACTATTCCAGGGCCCTCTCCACCACTCCAGGGCCCTCTCCACTATTCCAGGGCCCTCTCCACCACCCCAGGGCCCTCTCCACCACCCCAGGGCCCTCTCCACTATTCCAGGGCCCTCTCCACCACCCCAGGGCCCTCTCCACTATTCCAGGGCCCTCTCCACCACC\t60\tPASS\tIMPRECISE;SVTYPE=INS;SVLEN=182;END=1285239;SUPPORT=3;COVERAGE=4,4,4,4,4;STRAND=+-;AF=0.75;STDEV_LEN=3.055;STDEV_POS=222.264;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.81SF|chr16;test_2_reheader_POS=Sniffles2.INS.81SF|1285239;test_2_reheader_QUAL=Sniffles2.INS.81SF|60;test_2_reheader_FILTERS=Sniffles2.INS.81SF|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.81SF|test_2|GT:0/1|GQ:1|DR:1|DV:3;test_2_reheader_INFO=Sniffles2.INS.81SF|IMPRECISE|SVTYPE:INS|SVLEN:182|END:1285239|SUPPORT:3|COVERAGE:4:4:4:4:4|STRAND:+-|AF:0.75|STDEV_LEN:3.055|STDEV_POS:222.264|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:1:1:3",
+                "chr16\t1308390\tSniffles2.DEL.91SF:test_1_reheader|Sniffles2.DEL.F1SF:test_2_reheader\ttgagtgagggagggaatgagtgagggagggaatgag\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-36;END=1308426;SUPPORT=12;COVERAGE=12,12,12,12,12;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.F1SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.91SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.F1SF|chr16;test_1_reheader_POS=Sniffles2.DEL.91SF|1308390;test_2_reheader_POS=Sniffles2.DEL.F1SF|1308390;test_1_reheader_QUAL=Sniffles2.DEL.91SF|60;test_2_reheader_QUAL=Sniffles2.DEL.F1SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.91SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.F1SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.91SF|test_1|GT:1/1|GQ:33|DR:0|DV:12;test_2_reheader_SAMPLE=Sniffles2.DEL.F1SF|test_2|GT:1/1|GQ:11|DR:3|DV:15;test_1_reheader_INFO=Sniffles2.DEL.91SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:1308426|SUPPORT:12|COVERAGE:12:12:12:12:12|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.F1SF|PRECISE|SVTYPE:DEL|SVLEN:-36|END:1308426|SUPPORT:15|COVERAGE:18:18:18:19:19|STRAND:+-|AF:0.833|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:33:0:12\t1/1:11:3:15",
+                "chr16\t1345656\tSniffles2.INS.5BSF:test_1_reheader|Sniffles2.INS.84SF:test_2_reheader\tN\tGCAACCCCAGCCTCCCCAGCCTCCCCAGCAACCCCAGCCTCCCCAGCAACCCCAGCCTCCTCA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=63;END=1345656;SUPPORT=14;COVERAGE=26,26,26,25,24;STRAND=+-;AF=0.538;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.84SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.5BSF|chr16;test_2_reheader_CHROM=Sniffles2.INS.84SF|chr16;test_1_reheader_POS=Sniffles2.INS.5BSF|1345656;test_2_reheader_POS=Sniffles2.INS.84SF|1345656;test_1_reheader_QUAL=Sniffles2.INS.5BSF|60;test_2_reheader_QUAL=Sniffles2.INS.84SF|60;test_1_reheader_FILTERS=Sniffles2.INS.5BSF|PASS;test_2_reheader_FILTERS=Sniffles2.INS.84SF|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.5BSF|test_1|GT:0/1|GQ:60|DR:12|DV:14;test_2_reheader_SAMPLE=Sniffles2.INS.84SF|test_2|GT:0/1|GQ:49|DR:11|DV:8;test_1_reheader_INFO=Sniffles2.INS.5BSF|PRECISE|SVTYPE:INS|SVLEN:63|END:1345656|SUPPORT:14|COVERAGE:26:26:26:25:24|STRAND:+-|AF:0.538|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.84SF|PRECISE|SVTYPE:INS|SVLEN:63|END:1345656|SUPPORT:8|COVERAGE:19:19:19:19:18|STRAND:+-|AF:0.421|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:60:12:14\t0/1:49:11:8",
+                "chr16\t1356874\tSniffles2.DEL.93SF:test_1_reheader|Sniffles2.DEL.F9SF:test_2_reheader\t.\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-42;END=1356916;SUPPORT=3;COVERAGE=6,5,5,5,5;STRAND=+-;AF=0.6;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.F9SF:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.93SF|chr16;test_2_reheader_CHROM=Sniffles2.DEL.F9SF|chr16;test_1_reheader_POS=Sniffles2.DEL.93SF|1356874;test_2_reheader_POS=Sniffles2.DEL.F9SF|1356874;test_1_reheader_QUAL=Sniffles2.DEL.93SF|60;test_2_reheader_QUAL=Sniffles2.DEL.F9SF|60;test_1_reheader_FILTERS=Sniffles2.DEL.93SF|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.F9SF|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.93SF|test_1|GT:0/1|GQ:11|DR:2|DV:3;test_2_reheader_SAMPLE=Sniffles2.DEL.F9SF|test_2|GT:0/1|GQ:23|DR:6|DV:4;test_1_reheader_INFO=Sniffles2.DEL.93SF|PRECISE|SVTYPE:DEL|SVLEN:-42|END:1356916|SUPPORT:3|COVERAGE:6:5:5:5:5|STRAND:+-|AF:0.6|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.F9SF|PRECISE|SVTYPE:DEL|SVLEN:-42|END:1356916|SUPPORT:4|COVERAGE:10:10:10:10:8|STRAND:+-|AF:0.4|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:11:2:3\t0/1:23:6:4",
+                "chr16\t1367562\tSniffles2.DEL.FASF\t.\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-53;END=1367615;SUPPORT=2;COVERAGE=3,3,3,3,3;STRAND=+-;AF=0.667;STDEV_LEN=2.121;STDEV_POS=5.657;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.DEL.FASF|chr16;test_2_reheader_POS=Sniffles2.DEL.FASF|1367562;test_2_reheader_QUAL=Sniffles2.DEL.FASF|60;test_2_reheader_FILTERS=Sniffles2.DEL.FASF|PASS;test_2_reheader_SAMPLE=Sniffles2.DEL.FASF|test_2|GT:0/1|GQ:4|DR:1|DV:2;test_2_reheader_INFO=Sniffles2.DEL.FASF|PRECISE|SVTYPE:DEL|SVLEN:-53|END:1367615|SUPPORT:2|COVERAGE:3:3:3:3:3|STRAND:+-|AF:0.667|STDEV_LEN:2.121|STDEV_POS:5.657|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:4:1:2",
+                "chr20\t2659083\tSniffles2.INS.0S13:test_1_reheader|Sniffles2.INS.0S13:test_2_reheader\tN\tGCAGATCAGAGGCAGGATGTGGCTACCGAGCAGGCAAAGATGATGGGAAAT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=51;END=2659083;SUPPORT=8;COVERAGE=21,18,18,18,18;STRAND=+-;AF=0.444;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.0S13:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.0S13|chr20;test_2_reheader_CHROM=Sniffles2.INS.0S13|chr20;test_1_reheader_POS=Sniffles2.INS.0S13|2659083;test_2_reheader_POS=Sniffles2.INS.0S13|2659083;test_1_reheader_QUAL=Sniffles2.INS.0S13|60;test_2_reheader_QUAL=Sniffles2.INS.0S13|60;test_1_reheader_FILTERS=Sniffles2.INS.0S13|PASS;test_2_reheader_FILTERS=Sniffles2.INS.0S13|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.0S13|test_1|GT:0/1|GQ:52|DR:10|DV:8;test_2_reheader_SAMPLE=Sniffles2.INS.0S13|test_2|GT:0/1|GQ:60|DR:18|DV:12;test_1_reheader_INFO=Sniffles2.INS.0S13|PRECISE|SVTYPE:INS|SVLEN:51|END:2659083|SUPPORT:8|COVERAGE:21:18:18:18:18|STRAND:+-|AF:0.444|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.0S13|PRECISE|SVTYPE:INS|SVLEN:51|END:2659083|SUPPORT:12|COVERAGE:30:30:30:30:29|STRAND:+-|AF:0.4|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t0/1:52:10:8\t0/1:60:18:12",
+                "chrX\t3036626\tSniffles2.DEL.2S16\ttatatataatatatataatattttatataaaatat\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-35;END=3036661;SUPPORT=2;COVERAGE=7,7,7,7,6;STRAND=+-;AF=0.286;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.2S16|chrX;test_1_reheader_POS=Sniffles2.DEL.2S16|3036626;test_1_reheader_QUAL=Sniffles2.DEL.2S16|60;test_1_reheader_FILTERS=Sniffles2.DEL.2S16|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.2S16|test_1|GT:0/1|GQ:6|DR:5|DV:2;test_1_reheader_INFO=Sniffles2.DEL.2S16|PRECISE|SVTYPE:DEL|SVLEN:-35|END:3036661|SUPPORT:2|COVERAGE:7:7:7:7:6|STRAND:+-|AF:0.286|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:6:5:2\t./.:.:.:.",
+                "chrX\t3037125\tSniffles2.DEL.5S16\ttataatattatatataaaatatatataatatatata\tN\t60\tPASS\tIMPRECISE;SVTYPE=DEL;SVLEN=-36;END=3037161;SUPPORT=3;COVERAGE=7,6,6,6,5;STRAND=+-;AF=0.5;STDEV_LEN=6.928;STDEV_POS=45.033;FOUND_IN=sniffles;set=test_1_reheader;FOUNDBY=1;test_1_reheader_CHROM=Sniffles2.DEL.5S16|chrX;test_1_reheader_POS=Sniffles2.DEL.5S16|3037125;test_1_reheader_QUAL=Sniffles2.DEL.5S16|60;test_1_reheader_FILTERS=Sniffles2.DEL.5S16|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.5S16|test_1|GT:0/1|GQ:21|DR:3|DV:3;test_1_reheader_INFO=Sniffles2.DEL.5S16|IMPRECISE|SVTYPE:DEL|SVLEN:-36|END:3037161|SUPPORT:3|COVERAGE:7:6:6:6:5|STRAND:+-|AF:0.5|STDEV_LEN:6.928|STDEV_POS:45.033|FOUND_IN:sniffles;svdb_origin=test_1_reheader;SUPP_VEC=10\tGT:GQ:DR:DV\t0/1:21:3:3\t./.:.:.:.",
+                "chrX\t3080256\tSniffles2.DEL.6S16:test_1_reheader|Sniffles2.DEL.9S16:test_2_reheader\tatgaggtccggagatgcagaccatcctggccaacatg\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-37;END=3080293;SUPPORT=12;COVERAGE=12,12,12,12,12;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.9S16:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.6S16|chrX;test_2_reheader_CHROM=Sniffles2.DEL.9S16|chrX;test_1_reheader_POS=Sniffles2.DEL.6S16|3080256;test_2_reheader_POS=Sniffles2.DEL.9S16|3080256;test_1_reheader_QUAL=Sniffles2.DEL.6S16|60;test_2_reheader_QUAL=Sniffles2.DEL.9S16|60;test_1_reheader_FILTERS=Sniffles2.DEL.6S16|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.9S16|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.6S16|test_1|GT:1/1|GQ:33|DR:0|DV:12;test_2_reheader_SAMPLE=Sniffles2.DEL.9S16|test_2|GT:1/1|GQ:8|DR:0|DV:3;test_1_reheader_INFO=Sniffles2.DEL.6S16|PRECISE|SVTYPE:DEL|SVLEN:-37|END:3080293|SUPPORT:12|COVERAGE:12:12:12:12:12|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.9S16|PRECISE|SVTYPE:DEL|SVLEN:-37|END:3080293|SUPPORT:3|COVERAGE:3:3:3:3:3|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:33:0:12\t1/1:8:0:3",
+                "chrX\t9964280\tSniffles2.DEL.7S16:test_1_reheader|Sniffles2.DEL.CS16:test_2_reheader\tccttccttccttccttccttccttccttccttccttccttcctt\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-44;END=9964324;SUPPORT=19;COVERAGE=19,19,19,19,19;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;FOUND_IN=sniffles;VARID=Sniffles2.DEL.CS16:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.7S16|chrX;test_2_reheader_CHROM=Sniffles2.DEL.CS16|chrX;test_1_reheader_POS=Sniffles2.DEL.7S16|9964280;test_2_reheader_POS=Sniffles2.DEL.CS16|9964280;test_1_reheader_QUAL=Sniffles2.DEL.7S16|60;test_2_reheader_QUAL=Sniffles2.DEL.CS16|60;test_1_reheader_FILTERS=Sniffles2.DEL.7S16|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.CS16|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.7S16|test_1|GT:1/1|GQ:52|DR:0|DV:19;test_2_reheader_SAMPLE=Sniffles2.DEL.CS16|test_2|GT:1/1|GQ:36|DR:0|DV:13;test_1_reheader_INFO=Sniffles2.DEL.7S16|PRECISE|SVTYPE:DEL|SVLEN:-44|END:9964324|SUPPORT:19|COVERAGE:19:19:19:19:19|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.CS16|PRECISE|SVTYPE:DEL|SVLEN:-44|END:9964324|SUPPORT:13|COVERAGE:13:13:13:13:13|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:52:0:19\t1/1:36:0:13",
+                "chrX\t11163883\tSniffles2.INS.0S16:test_1_reheader|Sniffles2.INS.1S16:test_2_reheader\tN\tAAAGAAATCAGCAGTCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAAGAGATCGAGACCATCCCGGCTAAAACGGTGAAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=316;END=11163883;SUPPORT=4;COVERAGE=3,4,4,4,4;STRAND=+-;AF=1;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;VARID=Sniffles2.INS.1S16:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.INS.0S16|chrX;test_2_reheader_CHROM=Sniffles2.INS.1S16|chrX;test_1_reheader_POS=Sniffles2.INS.0S16|11163883;test_2_reheader_POS=Sniffles2.INS.1S16|11163883;test_1_reheader_QUAL=Sniffles2.INS.0S16|60;test_2_reheader_QUAL=Sniffles2.INS.1S16|60;test_1_reheader_FILTERS=Sniffles2.INS.0S16|PASS;test_2_reheader_FILTERS=Sniffles2.INS.1S16|PASS;test_1_reheader_SAMPLE=Sniffles2.INS.0S16|test_1|GT:1/1|GQ:11|DR:0|DV:4;test_2_reheader_SAMPLE=Sniffles2.INS.1S16|test_2|GT:1/1|GQ:8|DR:0|DV:3;test_1_reheader_INFO=Sniffles2.INS.0S16|PRECISE|SVTYPE:INS|SVLEN:316|END:11163883|SUPPORT:4|COVERAGE:3:4:4:4:4|STRAND:+-|AF:1|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.INS.1S16|PRECISE|SVTYPE:INS|SVLEN:318|END:11163883|SUPPORT:3|COVERAGE:3:3:3:3:4|STRAND:+-|AF:1|STDEV_LEN:2.646|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:11:0:4\t1/1:8:0:3",
+                "chrX\t12621974\tSniffles2.DEL.9S16:test_1_reheader|Sniffles2.DEL.14S16:test_2_reheader\tgaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaaagaaggaaagaaagaaggaaagaagaagaaaagaggagaagagaggagaggaaaggagaggagaggagaggagaggtgaactataaaaagaaccaaacagaaatcctggagctaaagaatacaatgacaaaactaaacattttaatagcttcaacagcagactcaattatgcagaagaatcagcaaatgtgaagacaggctatttgaaattacccagttagaggaacagaaagtaaaaagaataaaaaagagtaaaggaagcatacaggtcctatgagataccatcaattgaatgaatatatgcattatgggaatattagaaggagaaaaggaaaaaaggggaaaaagcttatttaaagaaataatggctgaaacgtcctaaatcttggaagggatatggacatccagatttatacaaatcaaagggtctcaagcagaatcaatccaaagactactctaagacacattataaccaaatttttaaaagccaaacacagacatagaatattgcccctaagagatatcatttgagatatataaattacatgaaaaataatacaaaataatcaccttaatgaagctcagtgggatacaagagaacacagaccaccaagaaaaacaaaaagcaatacataaacaaaataaaaagtttaataaagaaatacaggtcaggcgtggtgattcacatttgtaattccagcactttgggaggccaaggcaggcagatggctttgagcccaaaagttcaagactagcctgggcaacatggcaaaaccccatctctacaaaaattagccagatgtggtggcccgaatctgtagtcccagcaacttgggaggctgaggtgggaggatgacttgagcccaggaggcagaggtttcagtgagccaagatcacaccactgcactgtagcctgggcaacatagccagaccctgtttcaaaaaaagaaaagaaaagaaaggaaaaaggaaaggaagtaataaggaaaggaaaaaggaaaggaagggaagggaagtgaagggaagggaagtgaagggaagggaaaggaagggaggaagaaagaaagaaagagagagagagagaaagaaagaaagagaaagaa\tN\t60\tPASS\tPRECISE;SVTYPE=DEL;SVLEN=-1191;END=12623165;SUPPORT=5;COVERAGE=7,7,6,6,6;STRAND=+-;AF=0.833;STDEV_LEN=0.577;STDEV_POS=2.309;FOUND_IN=sniffles;IMPRECISE;VARID=Sniffles2.DEL.14S16:test_2_reheader;set=Intersection;FOUNDBY=2;test_1_reheader_CHROM=Sniffles2.DEL.9S16|chrX;test_2_reheader_CHROM=Sniffles2.DEL.14S16|chrX;test_1_reheader_POS=Sniffles2.DEL.9S16|12621974;test_2_reheader_POS=Sniffles2.DEL.14S16|12622162;test_1_reheader_QUAL=Sniffles2.DEL.9S16|60;test_2_reheader_QUAL=Sniffles2.DEL.14S16|60;test_1_reheader_FILTERS=Sniffles2.DEL.9S16|PASS;test_2_reheader_FILTERS=Sniffles2.DEL.14S16|PASS;test_1_reheader_SAMPLE=Sniffles2.DEL.9S16|test_1|GT:1/1|GQ:3|DR:1|DV:5;test_2_reheader_SAMPLE=Sniffles2.DEL.14S16|test_2|GT:1/1|GQ:20|DR:1|DV:11;test_1_reheader_INFO=Sniffles2.DEL.9S16|PRECISE|SVTYPE:DEL|SVLEN:-1191|END:12623165|SUPPORT:5|COVERAGE:7:7:6:6:6|STRAND:+-|AF:0.833|STDEV_LEN:0.577|STDEV_POS:2.309|FOUND_IN:sniffles;test_2_reheader_INFO=Sniffles2.DEL.14S16|IMPRECISE|SVTYPE:DEL|SVLEN:-1187|END:12623349|SUPPORT:11|COVERAGE:13:12:12:12:12|STRAND:+-|AF:0.917|STDEV_LEN:2.582|STDEV_POS:142.789|FOUND_IN:sniffles;svdb_origin=test_1_reheader|test_2_reheader;SUPP_VEC=11\tGT:GQ:DR:DV\t1/1:3:1:5\t1/1:20:1:11",
+                "chrX\t14631916\tSniffles2.INS.4S16\tN\tATATGTATATGTATATATATAGACATACATATGTATATGTCTATATAGACATACATATACGTATGTCTATATAGACATACATATACGTATGTCTATATAGACATACATATATGTATGTCTATATACAAGACATATATATCTATATATACACATATACGTATATATAGACATATACGTATATGTGTATATATAGACATATACGTATATGTGTATATATAGACATATACGTATATGTGTATATATAGACATATATATGTATATGTGTAT\t60\tPASS\tPRECISE;SVTYPE=INS;SVLEN=267;END=14631916;SUPPORT=3;COVERAGE=4,4,4,2,1;STRAND=+-;AF=0.75;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0;FOUND_IN=sniffles;set=test_2_reheader;FOUNDBY=1;test_2_reheader_CHROM=Sniffles2.INS.4S16|chrX;test_2_reheader_POS=Sniffles2.INS.4S16|14631916;test_2_reheader_QUAL=Sniffles2.INS.4S16|60;test_2_reheader_FILTERS=Sniffles2.INS.4S16|PASS;test_2_reheader_SAMPLE=Sniffles2.INS.4S16|test_2|GT:0/1|GQ:1|DR:1|DV:3;test_2_reheader_INFO=Sniffles2.INS.4S16|PRECISE|SVTYPE:INS|SVLEN:267|END:14631916|SUPPORT:3|COVERAGE:4:4:4:2:1|STRAND:+-|AF:0.75|STDEV_LEN:0|STDEV_POS:0|SUPPORT_LONG:0|FOUND_IN:sniffles;svdb_origin=test_2_reheader;SUPP_VEC=01\tGT:GQ:DR:DV\t./.:.:.:.\t0/1:1:1:3"
+            ],
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:26:28.586336982"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], bed - sniffles -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:29:17.841219039"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], [] - severus -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:29:47.72768953"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], [] - sniffles": {
+        "content": [
+            "7cd0730159250c8945e2007da414651e",
+            "46a46d863d6d0d0ac83778dfbf4e969f",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:25:50.038358587"
+    },
+    "1 sample - [bam, bai], fasta, fai, bed, [] - severus": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]",
+            "d64a5438fe54c0239613976f8826897b",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=53, phased=false, phasedAutodetect=false]",
+            "c37e6c17e6d1ccf07c23476f13c3e5ef",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:27:21.812768584"
+    },
+    "1 sample - [bam, bai], fasta, fai, [], bed - sniffles": {
+        "content": [
+            "7cd0730159250c8945e2007da414651e",
+            "46a46d863d6d0d0ac83778dfbf4e969f",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:26:44.491561807"
+    },
+    "2 samples - [bam, bai], fasta, fai, [], [] - severus -stub": {
+        "content": [
+            "[test_1_reheader.vcf.gz, test_2_reheader.vcf.gz]",
+            [
+                [
+                    {
+                        "id": "test_1",
+                        "single_end": false,
+                        "family_id": "family"
+                    },
+                    "test_1_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                [
+                    {
+                        "id": "test_2",
+                        "single_end": false,
+                        "family_id": "family"
+                    },
+                    "test_2_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "family"
+                    },
+                    "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "family"
+                    },
+                    "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:30:32.349238883"
+    },
+    "1 sample - [bam, bai], fasta, fai, bed, [] - severus -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                ],
+                "family_tbi": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_vcf": [
+                    [
+                        {
+                            "id": "family"
+                        },
+                        "family_svs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "sample_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sample_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false,
+                            "family_id": "family"
+                        },
+                        "test_reheader.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                    "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                    "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                    "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:30:16.946977312"
+    },
+    "2 samples - [bam, bai], fasta, fai, [], [] - severus": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=56, phased=false, phasedAutodetect=false]",
+            "1294e2ab468789a0bd56e8bcaf578a4",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=71, phased=false, phasedAutodetect=false]",
+            "1c9a74feb498450766db003698579ded",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=2, variantCount=80, phased=false, phasedAutodetect=false]",
+            "bb2aa63da770c7f58eb5efa1a36101b8",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c",
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:28:33.091100608"
+    },
+    "1 sample - [bam, bai], fasta, fai, bed, [] - sniffles": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=84, phased=false, phasedAutodetect=false]",
+            "3cb4ba0bf05ab17ef02c4b51e70e4e6e",
+            "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=83, phased=false, phasedAutodetect=false]",
+            "e1908dac54d273f92eb06162a574a217",
+            [
+                "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
+                "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
+                "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
+                "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
+                "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                "versions.yml:md5,cff333ea42eb748bf5dcc2c2a7d59c5f",
+                "versions.yml:md5,d6665112b721f1651ae340c644f9a27c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-21T14:26:07.339172165"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/call_svs/tests/nextflow.config b/subworkflows/local/call_svs/tests/nextflow.config
new file mode 100644
index 00000000..6065d7ee
--- /dev/null
+++ b/subworkflows/local/call_svs/tests/nextflow.config
@@ -0,0 +1,33 @@
+process {
+
+    withName: 'ADD_FOUND_IN_TAG' {
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type b',
+            '--write-index=csi',
+            '--no-version'
+        ].join(' ')
+    }
+
+    withName: 'CALL_SVS:SVDB_MERGE' {
+        ext.prefix = { "${meta.id}_svs" }
+        ext.args = [
+            '--bnd_distance 1000',
+            '--overlap .5'
+        ].join(' ')
+        ext.args2 = '--no-version'
+    }
+
+    withName: 'BCFTOOLS_QUERY' {
+        ext.args = '--list-samples'
+    }
+
+    withName: 'CREATE_SAMPLES_FILE' {
+        ext.prefix = { "${meta.id}_samples_file" }
+    }
+
+    withName: 'BCFTOOLS_REHEADER' {
+        ext.prefix = { "${meta.id}_reheader" }
+        ext.args2 = '--output-type z --write-index=tbi --no-version'
+    }
+}
diff --git a/subworkflows/local/cnv.nf b/subworkflows/local/cnv.nf
deleted file mode 100644
index 5da2d417..00000000
--- a/subworkflows/local/cnv.nf
+++ /dev/null
@@ -1,51 +0,0 @@
-include { HIFICNV                      } from '../../modules/local/pacbio/hificnv'
-include { TABIX_TABIX as TABIX_HIFICNV } from '../../modules/nf-core/tabix/tabix/'
-
-workflow CNV {
-
-    take:
-    ch_bam_bai_vcf // channel: [ val(meta), [[ bam ], [bai], [vcf] ]
-    ch_fasta
-    ch_expected_xy_bed
-    ch_expected_xx_bed
-    ch_exclude_bed
-
-    main:
-    ch_versions     = Channel.empty()
-
-    // Split samples if male or female
-    ch_bam_bai_vcf
-        .branch{ meta, bam, bai, vcf ->
-            male:   meta.sex == 1
-            female: meta.sex == 2
-        }
-        .set{branched_bam}
-
-    // Then merge male with XY-bed
-    branched_bam
-        .male
-        .combine(ch_expected_xy_bed)
-        .set {branched_bam_male}
-
-    // And female with XX-bed
-    branched_bam
-        .female
-        .combine(ch_expected_xx_bed)
-        .set {branched_bam_female}
-
-    // Concatenate the two channels
-    branched_bam_male
-        .concat(branched_bam_female)
-        .set{ ch_hificnv_in }
-
-    // Run HiFiCNV
-    HIFICNV(ch_hificnv_in, ch_fasta, ch_exclude_bed)
-    ch_versions = ch_versions.mix(HIFICNV.out.versions)
-
-    TABIX_HIFICNV(HIFICNV.out.vcf)
-    ch_versions = ch_versions.mix(TABIX_HIFICNV.out.versions)
-
-    emit:
-    versions = ch_versions                  // channel: [ versions.yml ]
-}
-
diff --git a/subworkflows/local/convert_input_files.nf b/subworkflows/local/convert_input_files.nf
index 5c44e521..0cd46bf2 100644
--- a/subworkflows/local/convert_input_files.nf
+++ b/subworkflows/local/convert_input_files.nf
@@ -4,7 +4,9 @@ include { SAMTOOLS_FASTQ } from '../../modules/nf-core/samtools/fastq/main'
 workflow CONVERT_INPUT_FILES {
 
     take:
-    ch_sample // channel: [ val(meta), reads ]
+    ch_sample     // channel: [ val(meta), reads ]
+    convert_bam   // bool
+    convert_fastq // bool
 
     main:
     ch_versions = Channel.empty()
@@ -19,15 +21,20 @@ workflow CONVERT_INPUT_FILES {
     ch_bam   = ch_filetypes.bam
     ch_fastq = ch_filetypes.fastq
 
-    SAMTOOLS_FASTQ ( ch_filetypes.bam, false )
-    ch_versions = ch_versions.mix(SAMTOOLS_FASTQ.out.versions)
+    if(convert_bam) {
+        SAMTOOLS_FASTQ ( ch_filetypes.bam, false )
+        ch_versions = ch_versions.mix(SAMTOOLS_FASTQ.out.versions)
 
-    SAMTOOLS_IMPORT ( ch_filetypes.fastq )
-    ch_versions = ch_versions.mix(SAMTOOLS_IMPORT.out.versions)
+        // Mix converted files back in
+        ch_fastq = ch_fastq.mix(SAMTOOLS_FASTQ.out.other)
+    }
+    if(convert_fastq) {
+        SAMTOOLS_IMPORT ( ch_filetypes.fastq )
+        ch_versions = ch_versions.mix(SAMTOOLS_IMPORT.out.versions)
 
-    // Mix converted files back in
-    ch_bam   = ch_bam.mix(SAMTOOLS_IMPORT.out.bam)
-    ch_fastq = ch_fastq.mix(SAMTOOLS_FASTQ.out.other)
+        // Mix converted files back in
+        ch_bam   = ch_bam.mix(SAMTOOLS_IMPORT.out.bam)
+    }
 
     emit:
     bam      = ch_bam      // channel: [ val(meta), bam ]
diff --git a/subworkflows/local/filter_variants/main.nf b/subworkflows/local/filter_variants/main.nf
new file mode 100644
index 00000000..dd87ddf9
--- /dev/null
+++ b/subworkflows/local/filter_variants/main.nf
@@ -0,0 +1,39 @@
+include { ENSEMBLVEP_FILTERVEP          } from '../../../modules/nf-core/ensemblvep/filtervep/main'
+include { BCFTOOLS_VIEW                 } from '../../../modules/nf-core/bcftools/view/main'
+include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep/main.nf'
+
+workflow FILTER_VARIANTS {
+
+    take:
+    ch_vcf      // channel  [optional] [ val(meta), path(vcf) ]
+    ch_hgnc_ids // channel: [optional] [ val(meta), path(txt) ]
+    filter_hgnc //    bool: should filter_vep be run to filter on hgnc ids
+
+    main:
+    ch_versions = Channel.empty()
+
+    if ( filter_hgnc ) {
+
+        ENSEMBLVEP_FILTERVEP (
+            ch_vcf,
+            ch_hgnc_ids.map { meta, file -> file }
+        )
+        ch_versions = ch_versions.mix(ENSEMBLVEP_FILTERVEP.out.versions)
+
+        ch_vcf = ENSEMBLVEP_FILTERVEP.out.output
+    }
+
+    BCFTOOLS_VIEW (
+        ch_vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        [],
+        [],
+        []
+    )
+    ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions)
+
+    emit:
+    vcf      = BCFTOOLS_VIEW.out.vcf // channel: [ val(meta), path(vcf) ]
+    tbi      = BCFTOOLS_VIEW.out.tbi // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions           // channel: [ path(versions.yml) ]
+}
+
diff --git a/subworkflows/local/filter_variants/tests/main.nf.test b/subworkflows/local/filter_variants/tests/main.nf.test
new file mode 100644
index 00000000..692cf9ec
--- /dev/null
+++ b/subworkflows/local/filter_variants/tests/main.nf.test
@@ -0,0 +1,150 @@
+nextflow_workflow {
+
+    name "Test Workflow FILTER_VARIANTS"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "FILTER_VARIANTS"
+
+    setup {
+        run("GUNZIP") {
+            script "../../../../modules/nf-core/gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'hg38' ],
+                    file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        run("SAMTOOLS_FAIDX") {
+            script "../../../../modules/nf-core/samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        run("MINIMAP2_ALIGN") {
+            script "../../../../modules/nf-core/minimap2/align/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', num_intervals:1 ],
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = true
+                input[3] = 'csi'
+                input[4] = false
+                input[5] = false
+                """
+            }
+        }
+
+        run("SHORT_VARIANT_CALLING") {
+            script "../../short_variant_calling/main.nf"
+            process {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                    .join(MINIMAP2_ALIGN.out.index)
+                    .join(Channel.of([
+                        [ id: 'test', num_intervals:1 ],
+                            file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkifexists: true)
+                    ]))
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+            """
+            }
+        }
+        run("UNTAR") {
+            script "../../../../modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'vep_cache' ],
+                    file(params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz', checkIfExists:true)
+                ]
+                """
+            }
+        }
+        run("SNV_ANNOTATION") {
+            script "../../snv_annotation/main.nf"
+            process {
+                """
+                input[0] = SHORT_VARIANT_CALLING.out.combined_bcf
+                input[1] = [
+                    file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true)
+                ]
+                input[2] = GUNZIP.out.gunzip
+                input[3] = SAMTOOLS_FAIDX.out.fai
+                input[4] = UNTAR.out.untar.map { meta, cache -> cache}
+                input[5] = Channel.value('110')
+                input[6] = Channel.of([
+                    file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
+                ]).splitCsv(header:true).map { row -> row.vep_files }.collect()
+                input[7] = false
+                input[8] = Channel.value([])
+                input[9] = null
+                input[10] = null
+            """
+            }
+        }
+    }
+
+    test("vcf, [[],[]], false") {
+
+        when {
+            workflow {
+                """
+                input[0] = SNV_ANNOTATION.out.vcf
+                input[1] = Channel.of([[],[]])
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.versions,
+                    file(workflow.out.tbi.get(0).get(1)).name,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.summary,
+                ).match() }
+            )
+        }
+    }
+
+    test("vcf, hgnc_ids, true") {
+        tag "hgnc"
+        when {
+            workflow {
+                """
+                input[0] = SNV_ANNOTATION.out.vcf
+                input[1] = Channel.of('HGNC:4826')
+                    .collectFile(name: 'hgnc_ids.txt')
+                    .map { file -> [ [ id: 'hgnc_ids' ], file ] }
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.versions,
+                    file(workflow.out.tbi.get(0).get(1)).name,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.summary,
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/filter_variants/tests/main.nf.test.snap b/subworkflows/local/filter_variants/tests/main.nf.test.snap
new file mode 100644
index 00000000..75153877
--- /dev/null
+++ b/subworkflows/local/filter_variants/tests/main.nf.test.snap
@@ -0,0 +1,33 @@
+{
+    "vcf, [[],[]], false": {
+        "content": [
+            [
+                "versions.yml:md5,c6563ccec6867a29e00bdbb19abee900"
+            ],
+            "test_data.bed_filtered.vcf.gz.tbi",
+            "28024aed73c5c0fd09c14cf32008a335",
+            "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=80, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-06T15:09:53.145300431"
+    },
+    "vcf, hgnc_ids, true": {
+        "content": [
+            [
+                "versions.yml:md5,24b641f905e26c567657e04d22f2e337",
+                "versions.yml:md5,c6563ccec6867a29e00bdbb19abee900"
+            ],
+            "test_data.bed_filtered.vcf.gz.tbi",
+            "77c14f11bd3af0802b1736cd87b949eb",
+            "VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=49, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-06T16:37:39.828165612"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/filter_variants/tests/nextflow.config b/subworkflows/local/filter_variants/tests/nextflow.config
new file mode 100644
index 00000000..b9fd0da1
--- /dev/null
+++ b/subworkflows/local/filter_variants/tests/nextflow.config
@@ -0,0 +1,80 @@
+process {
+    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT' {
+        ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
+        ext.args = { [
+            '--model_type PACBIO',
+            "--sample_name=${meta.id}",
+            '-vcf_stats_report=False'
+        ].join(' ') }
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:GLNEXUS' {
+        ext.args = '--config DeepVariant_unfiltered'
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT' {
+        ext.prefix = { "${meta.id}_concat" }
+        ext.args = [
+            '--no-version',
+            '--allow-overlaps'
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_MULTISAMPLE' {
+        ext.prefix = { "${meta.id}_norm_multisample" }
+        ext.args = [
+            '--no-version',
+            '-m -',
+            '--output-type u',
+            '--write-index=csi',
+            '-w 10000'
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_SINGLESAMPLE' {
+        ext.prefix = { "${meta.id}_norm_singlesample" }
+        ext.args = [
+            '--no-version',
+            '-m -',
+            '-w 10000',
+            '--output-type u',
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
+        ext.prefix = { "${meta.id}_ac" }
+        ext.args = [
+            '--no-version',
+            '--output-type u'
+        ].join(' ')
+    }
+
+    withName: 'SNV_ANNOTATION:BCFTOOLS_FILLTAGS_ANNO' {
+        ext.prefix = { "${meta.id}_filltags_anno" }
+        ext.args = [
+            '--no-version',
+            '--output-type z'
+        ].join(' ')
+    }
+
+    withName: 'UNTAR' {
+        ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' }
+    }
+
+    withName: 'SNV_ANNOTATION:ENSEMBLVEP_SNV' {
+        ext.args = { [
+            '--offline',
+            '--vcf',
+            '--compress_output bgzip'
+        ].join(' ') }
+    }
+
+    withName: 'FILTER_VARIANTS:ENSEMBLVEP_FILTERVEP' {
+        ext.args   = { "--filter \"HGNC_ID in ${feature_file}\"" }
+    }
+
+    withName: 'FILTER_VARIANTS:BCFTOOLS_VIEW' {
+        ext.prefix = { "${meta.id}_filtered" }
+        ext.args = '-e "INFO/AQ>60" --no-version --output-type z --write-index=tbi'
+    }
+}
diff --git a/subworkflows/local/genome_assembly.nf b/subworkflows/local/genome_assembly.nf
index 650af99f..2eebc358 100644
--- a/subworkflows/local/genome_assembly.nf
+++ b/subworkflows/local/genome_assembly.nf
@@ -13,17 +13,15 @@ workflow ASSEMBLY {
 
     main:
     ch_versions = Channel.empty()
+    ch_hifiasm_empty = Channel.value([ [], [], [] ])
 
     if(params.hifiasm_mode == 'hifi-only') {
 
         ch_reads
             .groupTuple()
-            .map{ meta, reads ->
-                [ meta, reads, [], [] ]
-            }
             .set { hifiasm_in }
 
-        HIFIASM ( hifiasm_in, [], [] )
+        HIFIASM ( hifiasm_in, ch_hifiasm_empty, ch_hifiasm_empty )
         ch_versions = ch_versions.mix(HIFIASM.out.versions)
 
     } else if(params.hifiasm_mode == 'trio-binning') {
@@ -98,7 +96,13 @@ workflow ASSEMBLY {
 
         hifiasm_trio_in = all_kid_reads.join(paternal_yak_or_empty).join(maternal_yak_or_empty)
 
-        HIFIASM ( hifiasm_trio_in, [], [] )
+        hifiasm_trio_in
+            .multiMap { meta, reads, paternal_yak, maternal_yak ->
+                reads : [meta, reads                     ]
+                yak   : [meta, paternal_yak, maternal_yak]
+            }
+            .set { ch_hifiasm_in }
+        HIFIASM ( ch_hifiasm_in.reads, ch_hifiasm_in.yak, ch_hifiasm_empty )
         ch_versions = ch_versions.mix(HIFIASM.out.versions)
     }
 
diff --git a/subworkflows/local/methylation.nf b/subworkflows/local/methylation.nf
deleted file mode 100644
index 6541a9f4..00000000
--- a/subworkflows/local/methylation.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-include { MODKIT_PILEUP as MODKIT_PILEUP_UNPHASED          } from '../../modules/nf-core/modkit/pileup/main'
-include { MODKIT_PILEUP as MODKIT_PILEUP_PHASED            } from '../../modules/nf-core/modkit/pileup/main'
-include { TABIX_BGZIPTABIX as BGZIP_MODKIT_PILEUP_UNPHASED } from '../../modules/nf-core/tabix/bgziptabix/main'
-include { TABIX_BGZIPTABIX as BGZIP_MODKIT_PILEUP_PHASED   } from '../../modules/nf-core/tabix/bgziptabix/main'
-
-workflow METHYLATION {
-
-    take:
-    ch_haplotagged_bam_bai // channel: [ val(meta), bam, bai ]
-    ch_fasta               // channel: [ val(meta), fasta ]
-    ch_fai                 // channel: [ val(meta), fai ]
-    ch_bed                 // channel: [ val(meta), bed ]
-
-    main:
-    ch_versions = Channel.empty()
-
-    // Run modkit pileup once without dividing by HP-tag and once with
-    MODKIT_PILEUP_UNPHASED (ch_haplotagged_bam_bai, ch_fasta, ch_bed)
-    ch_versions = ch_versions.mix(MODKIT_PILEUP_UNPHASED.out.versions)
-
-    MODKIT_PILEUP_PHASED (ch_haplotagged_bam_bai, ch_fasta, ch_bed)
-    ch_versions = ch_versions.mix(MODKIT_PILEUP_PHASED.out.versions)
-
-    // Bgzip and index output "BED"
-    BGZIP_MODKIT_PILEUP_UNPHASED ( MODKIT_PILEUP_UNPHASED.out.bed )
-    ch_versions = ch_versions.mix(BGZIP_MODKIT_PILEUP_UNPHASED.out.versions)
-
-    MODKIT_PILEUP_PHASED.out.bed
-        .transpose()
-        .set { ch_bgzip_modkit_pileup_phased_in }
-
-    BGZIP_MODKIT_PILEUP_PHASED ( ch_bgzip_modkit_pileup_phased_in )
-    ch_versions = ch_versions.mix(BGZIP_MODKIT_PILEUP_PHASED.out.versions)
-
-    emit:
-    versions = ch_versions // channel: [ versions.yml ]
-}
-
diff --git a/subworkflows/local/methylation/main.nf b/subworkflows/local/methylation/main.nf
new file mode 100644
index 00000000..261af3f1
--- /dev/null
+++ b/subworkflows/local/methylation/main.nf
@@ -0,0 +1,32 @@
+include { MODKIT_PILEUP    } from '../../../modules/nf-core/modkit/pileup/main'
+include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main'
+
+workflow METHYLATION {
+
+    take:
+    ch_bam_bai             // channel: [ val(meta), bam, bai ]
+    ch_fasta               // channel: [ val(meta), fasta ]
+    ch_fai                 // channel: [ val(meta), fai ]
+    ch_bed                 // channel: [ val(meta), bed ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    // Performs pileups per haplotype if the phasing workflow is on, set in config
+    MODKIT_PILEUP (ch_bam_bai, ch_fasta, ch_bed)
+    ch_versions = ch_versions.mix(MODKIT_PILEUP.out.versions)
+
+
+    MODKIT_PILEUP.out.bed
+        .transpose()
+        .set { ch_bgzip_modkit_pileup_in }
+
+    TABIX_BGZIPTABIX ( ch_bgzip_modkit_pileup_in )
+    ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
+
+    emit:
+    bed      = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, bed, tbi -> [ meta, bed ] } // channel: [ val(meta), path(bed) ]
+    tbi      = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, bed, tbi -> [ meta, tbi ] } // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/local/methylation/tests/main.nf.test b/subworkflows/local/methylation/tests/main.nf.test
new file mode 100644
index 00000000..4b72ed1c
--- /dev/null
+++ b/subworkflows/local/methylation/tests/main.nf.test
@@ -0,0 +1,261 @@
+nextflow_workflow {
+
+    name "Test Workflow METHYLATION"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "METHYLATION"
+
+    setup {
+        run("PREPARE_GENOME") {
+            script "../../prepare_genome.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'hg38' ],
+                    file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.empty()
+                input[2] = true
+                input[3] = false
+                """
+            }
+        }
+        run("MINIMAP2_ALIGN") {
+            script "../../../../modules/nf-core/minimap2/align/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', num_intervals:1 ],
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = true
+                input[3] = 'csi'
+                input[4] = false
+                input[5] = false
+                """
+            }
+        }
+        run("SHORT_VARIANT_CALLING") {
+            script "../../short_variant_calling/main.nf"
+            process {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                            .join(MINIMAP2_ALIGN.out.index)
+                            .join(Channel.of([
+                                [ id: 'test', num_intervals:1 ],
+                                file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkIfExists: true)
+                            ]))
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+            """
+            }
+        }
+        run("PHASING") {
+            script "../../phasing.nf"
+            process {
+                """
+                input[0] = SHORT_VARIANT_CALLING.out.snp_calls_vcf
+                input[1] = SHORT_VARIANT_CALLING.out.snp_calls_tbi
+                input[2] = MINIMAP2_ALIGN.out.bam
+                            .join(MINIMAP2_ALIGN.out.index)
+                            .map { meta, bam, bai ->
+                                [ [ id : meta.id ], bam, bai ]
+                            }
+                input[3] = PREPARE_GENOME.out.fasta
+                input[4] = PREPARE_GENOME.out.fai
+                """
+            }
+        }
+    }
+
+    test("1 sample - [] phased") {
+        when {
+            params {
+                skip_phasing = false
+            }
+            workflow {
+                """
+                input[0] = PHASING.out.haplotagged_bam_bai
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - [] unphased") {
+        when {
+            params {
+                skip_phasing = true
+            }
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index)
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - bed phased") {
+        when {
+            params {
+                skip_phasing = false
+            }
+            workflow {
+                """
+                input[0] = PHASING.out.haplotagged_bam_bai
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = Channel.of('chr20\t2650000\t2660000')
+                            .collectFile(name: 'chr20.bed', newLine: true)
+                            .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - bed unphased") {
+        when {
+            params {
+                skip_phasing = true
+            }
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index)
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = Channel.of('chr20\t2650000\t2660000')
+                            .collectFile(name: 'chr20.bed', newLine: true)
+                            .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - [] phased - stub") {
+        options "-stub"
+        when {
+            params {
+                skip_phasing = false
+            }
+            workflow {
+                """
+                input[0] = PHASING.out.haplotagged_bam_bai
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - bed phased - stub") {
+        options "-stub"
+        when {
+            params {
+                skip_phasing = false
+            }
+            workflow {
+                """
+                input[0] = PHASING.out.haplotagged_bam_bai
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = Channel.of('chr20\t2650000\t2660000')
+                            .collectFile(name: 'chr20.bed', newLine: true)
+                            .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - [] unphased - stub") {
+        options "-stub"
+        when {
+            params {
+                skip_phasing = true
+            }
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index)
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("1 sample - bed unphased - stub") {
+        options "-stub"
+        when {
+            params {
+                skip_phasing = true
+            }
+            workflow {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index)
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = Channel.of('chr20\t2650000\t2660000')
+                            .collectFile(name: 'chr20.bed', newLine: true)
+                            .map{ file -> [ [ id:'chr20'], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/methylation/tests/main.nf.test.snap b/subworkflows/local/methylation/tests/main.nf.test.snap
new file mode 100644
index 00000000..a96efcdf
--- /dev/null
+++ b/subworkflows/local/methylation/tests/main.nf.test.snap
@@ -0,0 +1,504 @@
+{
+    "1 sample - [] phased": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz:md5,b980e56ca6d65d09892b069a7d51b827"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_2.bed.gz:md5,32a5e2148266fefba8159d98f5f5dd87"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,bfeda9731d6d52508301ddf939302676"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,45800db86a2845fe961f536484369f61"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_2.bed.gz.tbi:md5,14f729ebf5ce7d265df85b21c30a67af"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,d08da21ae562fcc3c3361a916439c552"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz:md5,b980e56ca6d65d09892b069a7d51b827"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_2.bed.gz:md5,32a5e2148266fefba8159d98f5f5dd87"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,bfeda9731d6d52508301ddf939302676"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,45800db86a2845fe961f536484369f61"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_2.bed.gz.tbi:md5,14f729ebf5ce7d265df85b21c30a67af"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,d08da21ae562fcc3c3361a916439c552"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-01T16:42:19.164909715"
+    },
+    "1 sample - bed unphased - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T15:06:21.337874852"
+    },
+    "1 sample - [] unphased - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T15:05:51.048367417"
+    },
+    "1 sample - [] phased - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T15:32:25.389277494"
+    },
+    "1 sample - [] unphased": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,d3252e8b77241fe25edbcfd520b86159"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d34b6e7ed5a3010fba35ea9b58672dfd"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,d3252e8b77241fe25edbcfd520b86159"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d34b6e7ed5a3010fba35ea9b58672dfd"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-01T16:43:20.61904287"
+    },
+    "1 sample - bed phased": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz:md5,a0d9e7dd172fcbd0bbb19690b3570a3d"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,59353caa892772acc71cbdef07cca17d"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,1b46636405409529be7df321af87acd2"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,600db7bbfb1580cc2af629324e206045"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz:md5,a0d9e7dd172fcbd0bbb19690b3570a3d"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,59353caa892772acc71cbdef07cca17d"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,1b46636405409529be7df321af87acd2"
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,600db7bbfb1580cc2af629324e206045"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-01T16:44:23.18659219"
+    },
+    "1 sample - bed phased - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T15:32:58.055229101"
+    },
+    "1 sample - bed unphased": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,1bd6be90eb9c11b4cc9fa43dea4160ac"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,1983a3dfe9722ff9213cddcf6772d461"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz:md5,1bd6be90eb9c11b4cc9fa43dea4160ac"
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "num_intervals": 1
+                        },
+                        "test_modkit_pileup.bed.gz.tbi:md5,1983a3dfe9722ff9213cddcf6772d461"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,69dd5e76cc5e61cd0324b7412fc0546b",
+                    "versions.yml:md5,dc8e3f1d4b20b910f5148d89337e5711"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-01T16:45:25.026984417"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/methylation/tests/nextflow.config b/subworkflows/local/methylation/tests/nextflow.config
new file mode 100644
index 00000000..1152c16d
--- /dev/null
+++ b/subworkflows/local/methylation/tests/nextflow.config
@@ -0,0 +1,75 @@
+params {
+    preset = "pacbio"
+    phaser = "longphase"
+}
+
+process {
+
+    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
+        ext.args = { [
+            '--model_type PACBIO',
+            "--sample_name=${meta.id}",
+            '-vcf_stats_report=False'
+        ].join(' ') }
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT' {
+        ext.prefix = { "${meta.id}_concat" }
+        ext.args = [
+            '--no-version',
+            '--allow-overlaps'
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_SINGLESAMPLE' {
+        ext.prefix = { "${meta.id}_norm_singlesample" }
+        ext.args = [
+            '--no-version',
+            '-m -',
+            '-w 10000',
+            '--output-type z',
+            '--write-index=tbi',
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
+        ext.prefix = { "${meta.id}_ac" }
+        ext.args = [
+            '--no-version',
+            '--output-type u'
+        ].join(' ')
+    }
+
+    withName: 'MINIMAP2_ALIGN' {
+        ext.args = [
+            '-x map-hifi',
+            '-y'
+        ].join(' ')
+    }
+
+    withName: 'METHYLATION:MODKIT_PILEUP' {
+        ext.args = { [
+            '--combine-mods',
+            '--cpg',
+            '--combine-strands',
+            !params.skip_phasing ? '--partition-tag HP' : '',
+        ].join(' ') }
+        ext.prefix = { "${meta.id}_modkit_pileup" }
+    }
+
+    withName: 'METHYLATION:TABIX_BGZIPTABIX' {
+        ext.prefix = { "${input.simpleName}" }
+    }
+    withName: 'PHASING:LONGPHASE_PHASE' {
+        ext.prefix = { "${meta.id}_phased" }
+        ext.args = [
+            '--pb',
+            '--indels'
+        ].join(' ')
+    }
+
+    withName: 'PHASING:LONGPHASE_HAPLOTAG' {
+        ext.prefix = { "${meta.id}_haplotagged" }
+    }
+
+}
diff --git a/subworkflows/local/phasing.nf b/subworkflows/local/phasing.nf
index fb87a27b..4d3757ff 100644
--- a/subworkflows/local/phasing.nf
+++ b/subworkflows/local/phasing.nf
@@ -1,126 +1,138 @@
-include { BCFTOOLS_FILLFROMFASTA                       } from '../../modules/local/bcftools/fillfromfasta/main'
-include { BCFTOOLS_REHEADER                            } from '../../modules/nf-core/bcftools/reheader/main'
-include { CRAMINO as CRAMINO_PHASED                    } from '../../modules/local/cramino'
-include { HIPHASE as HIPHASE_SNV                       } from '../../modules/local/hiphase/main'
-include { HIPHASE as HIPHASE_SV                        } from '../../modules/local/hiphase/main'
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_WHATSHAP    } from '../../modules/nf-core/samtools/index/main'
-include { TABIX_BGZIPTABIX                             } from '../../modules/nf-core/tabix/bgziptabix/main'
-include { TABIX_TABIX                                  } from '../../modules/nf-core/tabix/tabix/main'
-include { WHATSHAP_HAPLOTAG                            } from '../../modules/local/whatshap/haplotag/main'
-include { WHATSHAP_PHASE                               } from '../../modules/local/whatshap/phase/main'
-include { WHATSHAP_STATS                               } from '../../modules/local/whatshap/stats/main'
+include { CRAMINO as CRAMINO_PHASED                  } from '../../modules/local/cramino'
+include { HIPHASE                                    } from '../../modules/local/hiphase/main'
+include { LONGPHASE_HAPLOTAG                         } from '../../modules/nf-core/longphase/haplotag/main'
+include { LONGPHASE_PHASE                            } from '../../modules/nf-core/longphase/phase/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_LONGPHASE } from '../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_WHATSHAP  } from '../../modules/nf-core/samtools/index/main'
+include { TABIX_TABIX as TABIX_LONGPHASE_PHASE       } from '../../modules/nf-core/tabix/tabix/main'
+include { WHATSHAP_HAPLOTAG                          } from '../../modules/local/whatshap/haplotag/main'
+include { WHATSHAP_PHASE                             } from '../../modules/local/whatshap/phase/main'
+include { WHATSHAP_STATS                             } from '../../modules/local/whatshap/stats/main'
 
 workflow PHASING {
     take:
-        ch_vcf     // channel: [ val(meta), vcf ]
-        ch_sv_vcf  // channel: [ val(meta), vcf ]
-        ch_bam_bai // channel: [ val(meta), bam, bai ]
-        fasta      // channel: [ val(meta), fasta ]
-        fai        // channel: [ val(meta), fai ]
+    ch_vcf       // channel: [ val(meta), path(vcf) ]
+    ch_vcf_index // channel: [ val(meta), path(tbi) ]
+    ch_bam_bai   // channel: [ val(meta), path(bam), path(bai) ]
+    fasta        // channel: [ val(meta), path(fasta) ]
+    fai          // channel: [ val(meta), path(fai) ]
 
     main:
-        ch_versions            = Channel.empty()
-        ch_bam_bai_haplotagged = Channel.empty()
-        ch_vcf_index           = Channel.empty()
-
-        TABIX_TABIX(ch_vcf)
-        ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
-
-        if (params.phaser.equals("whatshap")) {
-
-            WHATSHAP_PHASE( ch_vcf.join(ch_bam_bai), fasta, fai )
-            ch_versions = ch_versions.mix(WHATSHAP_PHASE.out.versions)
-
-            WHATSHAP_PHASE.out.vcf_tbi
-                .join(ch_bam_bai)
-                .set { ch_whatshap_haplotag_in }
-
-            WHATSHAP_HAPLOTAG(ch_whatshap_haplotag_in, fasta, fai)
-            ch_versions = ch_versions.mix(WHATSHAP_HAPLOTAG.out.versions)
-
-            SAMTOOLS_INDEX_WHATSHAP( WHATSHAP_HAPLOTAG.out.bam )
-            ch_versions = ch_versions.mix(SAMTOOLS_INDEX_WHATSHAP.out.versions)
-
-            WHATSHAP_HAPLOTAG
-                .out.bam
-                .join(SAMTOOLS_INDEX_WHATSHAP.out.bai)
-                .set { ch_bam_bai_haplotagged }
-
-            ch_vcf_index = ch_vcf_index.mix( WHATSHAP_PHASE.out.vcf_tbi )
-
-        } else if (params.phaser.equals("hiphase_snv")) {
-            ch_vcf
-                .join(TABIX_TABIX.out.csi)
-                .join(ch_bam_bai)
-                .set { ch_hiphase_snv_in }
-
-            HIPHASE_SNV( ch_hiphase_snv_in, fasta, fai, true )
-            ch_versions = ch_versions.mix(HIPHASE_SNV.out.versions)
-
-            HIPHASE_SNV.out.bams
-                .join(HIPHASE_SNV.out.bais)
-                .set { ch_bam_bai_haplotagged }
-
-            ch_vcf_index = ch_vcf_index.mix( HIPHASE_SNV.out.vcfs.join(HIPHASE_SNV.out.vcfs_tbi) )
-
-        } else if (params.phaser.equals("hiphase_sv")) {
-            // Sniffles specific...
-            BCFTOOLS_REHEADER(
-                ch_sv_vcf
-                    .map { meta, vcf -> [meta, vcf, [], []] },
-                [[],[]]
-            )
-            ch_versions = ch_versions.mix(BCFTOOLS_REHEADER.out.versions)
-
-            // Might be that newer versions of HiPhase ignores certain SVs
-            // if BCFTOOLS_FILLFROMFASTA is not run, instead of craching
-            BCFTOOLS_FILLFROMFASTA(BCFTOOLS_REHEADER.out.vcf, fasta)
-            ch_versions = ch_versions.mix(BCFTOOLS_FILLFROMFASTA.out.versions)
-
-            TABIX_BGZIPTABIX(BCFTOOLS_FILLFROMFASTA.out.vcf)
-            ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
-
-            TABIX_BGZIPTABIX.out.gz_tbi
-                .map { meta, gz, tbi -> [ meta, gz ] }
-                .set { ch_sv_vcf }
-
-            TABIX_BGZIPTABIX.out.gz_tbi
-                .map { meta, gz, tbi -> [ meta, tbi ] }
-                .set { ch_sv_tbi }
-
-            ch_vcf
-                .concat(ch_sv_vcf)
-                .groupTuple()
-                .set { ch_hiphase_vcf }
-
-            TABIX_TABIX.out.csi
-                .concat(ch_sv_tbi)
-                .groupTuple()
-                .set { ch_hiphase_tbi }
-
-            ch_hiphase_vcf
-                .join(ch_hiphase_tbi)
-                .join(ch_bam_bai)
-                .set { ch_hiphase_in }
-
-            HIPHASE_SV( ch_hiphase_in, fasta, fai, true )
-            ch_versions = ch_versions.mix(HIPHASE_SV.out.versions)
-
-            HIPHASE_SV.out.bams
-                .join(HIPHASE_SV.out.bais)
-                .set { ch_bam_bai_haplotagged }
-
-            ch_vcf_index = ch_vcf_index.mix( HIPHASE_SV.out.vcfs.join(HIPHASE_SV.out.vcfs_tbi) )
-        }
-
-        WHATSHAP_STATS( ch_vcf_index )
-        ch_versions = ch_versions.mix(WHATSHAP_STATS.out.versions)
-
-        CRAMINO_PHASED( ch_bam_bai_haplotagged )
-        ch_versions = ch_versions.mix(CRAMINO_PHASED.out.versions)
+    ch_versions            = Channel.empty()
+
+    // Phase variants and haplotag reads with Longphase
+    if (params.phaser.equals("longphase")) {
+
+        ch_bam_bai
+            .join( ch_vcf )
+            .map { meta, bam, bai, snvs -> [ meta, bam, bai, snvs, [], [] ] }
+            .set { ch_longphase_phase_in }
+
+        LONGPHASE_PHASE (
+            ch_longphase_phase_in,
+            fasta,
+            fai
+        )
+        ch_versions = ch_versions.mix(LONGPHASE_PHASE.out.versions)
+
+        TABIX_LONGPHASE_PHASE (
+            LONGPHASE_PHASE.out.vcf
+        )
+        ch_versions = ch_versions.mix(TABIX_LONGPHASE_PHASE.out.versions)
+
+        LONGPHASE_PHASE.out.vcf
+            .join( TABIX_LONGPHASE_PHASE.out.tbi )
+            .set { ch_phased_vcf_index }
+
+        ch_bam_bai
+            .join( LONGPHASE_PHASE.out.vcf )
+            .map { meta, bam, bai, vcf -> [ meta, bam, bai, vcf, [], [] ] }
+            .set { ch_longphase_haplotag_in }
+
+        LONGPHASE_HAPLOTAG (
+            ch_longphase_haplotag_in,
+            fasta,
+            fai
+        )
+        ch_versions = ch_versions.mix(LONGPHASE_HAPLOTAG.out.versions)
+
+        SAMTOOLS_INDEX_LONGPHASE (
+            LONGPHASE_HAPLOTAG.out.bam
+        )
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX_LONGPHASE.out.versions)
+
+        LONGPHASE_HAPLOTAG.out.bam
+            .join( SAMTOOLS_INDEX_LONGPHASE.out.bai )
+            .set { ch_bam_bai_haplotagged }
+
+    // Phase variants and haplotag reads with whatshap
+    } else if (params.phaser.equals("whatshap")) {
+
+        WHATSHAP_PHASE(
+            ch_vcf.join( ch_bam_bai ),
+            fasta,
+            fai
+        )
+        ch_versions = ch_versions.mix(WHATSHAP_PHASE.out.versions)
+
+        WHATSHAP_PHASE.out.vcf_tbi
+            .join( ch_bam_bai )
+            .set { ch_whatshap_haplotag_in }
+
+        WHATSHAP_HAPLOTAG (
+            ch_whatshap_haplotag_in,
+            fasta,
+            fai
+        )
+        ch_versions = ch_versions.mix(WHATSHAP_HAPLOTAG.out.versions)
+
+        SAMTOOLS_INDEX_WHATSHAP (
+            WHATSHAP_HAPLOTAG.out.bam
+        )
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX_WHATSHAP.out.versions)
+
+        WHATSHAP_HAPLOTAG.out.bam
+            .join( SAMTOOLS_INDEX_WHATSHAP.out.bai )
+            .set { ch_bam_bai_haplotagged }
+
+        WHATSHAP_PHASE.out.vcf_tbi
+            .set { ch_phased_vcf_index }
+
+    // Phase variants and haplotag reads with HiPhase
+    } else if (params.phaser.equals("hiphase")) {
+        ch_vcf
+            .join( ch_vcf_index )
+            .join( ch_bam_bai )
+            .set { ch_hiphase_snv_in }
+
+        HIPHASE (
+            ch_hiphase_snv_in,
+            fasta,
+            fai,
+            true
+        )
+        ch_versions = ch_versions.mix(HIPHASE.out.versions)
+
+        HIPHASE.out.bams
+            .join( HIPHASE.out.bais )
+            .set { ch_bam_bai_haplotagged }
+
+        HIPHASE.out.vcfs
+            .join( HIPHASE.out.vcfs_tbi )
+            .set { ch_phased_vcf_index }
+
+    }
+
+    // Phasing stats
+    WHATSHAP_STATS ( ch_phased_vcf_index )
+    ch_versions = ch_versions.mix(WHATSHAP_STATS.out.versions)
+
+    // Phasing QC
+    CRAMINO_PHASED ( ch_bam_bai_haplotagged )
+    ch_versions = ch_versions.mix(CRAMINO_PHASED.out.versions)
 
     emit:
-    haplotagged_bam_bai = ch_bam_bai_haplotagged   // channel: [ val(meta), bam, bai ]
-    stats               = WHATSHAP_STATS.out.stats // channel: [ val(meta), txt ]
-    versions            = ch_versions              // channel: [ versions.yml ]
+    haplotagged_bam_bai = ch_bam_bai_haplotagged   // channel: [ val(meta), path(bam), path(bai) ]
+    stats               = WHATSHAP_STATS.out.stats // channel: [ val(meta), path(txt) ]
+    versions            = ch_versions              // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index 1babff3b..31d88952 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -6,8 +6,10 @@ include { UNTAR as UNTAR_VEP_CACHE } from '../../modules/nf-core/untar/main'
 workflow PREPARE_GENOME {
 
     take:
-    fasta_in     // channel: [mandatory] [ val(meta), path(fasta) ]
-    ch_vep_cache // channel: [optional] [ path(cache) ]
+    fasta_in                   // channel: [ val(meta), path(fasta) ]
+    ch_vep_cache               // channel: [ val(meta), path(cache) ]
+    gunzip_fasta               // boolean: should we gunzip fasta
+    untar_vep_cache            // boolean: should we untar vep cache
 
     main:
     ch_versions = Channel.empty()
@@ -16,16 +18,15 @@ workflow PREPARE_GENOME {
     fasta_file = fasta_in.map{meta, file -> file}
 
     // Will not catch cases where fasta is bgzipped
-    if ( params.fasta.endsWith('.gz') ) {
-        GUNZIP_FASTA(fasta_in)
+    if ( gunzip_fasta ) {
+        GUNZIP_FASTA ( fasta_in )
             .gunzip
             .collect()
-            .set{ch_fasta}
-
+            .set { ch_fasta }
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions.first())
     } else {
         fasta_in
-            .set{ch_fasta}
+            .set { ch_fasta }
     }
 
     SAMTOOLS_FAIDX ( ch_fasta, [[],[]] )
@@ -34,18 +35,15 @@ workflow PREPARE_GENOME {
     MINIMAP2_INDEX ( ch_fasta )
     ch_versions = ch_versions.mix(MINIMAP2_INDEX.out.versions)
 
-    UNTAR_VEP_CACHE (ch_vep_cache)
-    ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions)
-
-    UNTAR_VEP_CACHE.out.untar
-        .map { meta, files -> [files] }
-        .collect()
-        .set { untarred_vep }
+    if (untar_vep_cache) {
+        UNTAR_VEP_CACHE (ch_vep_cache)
+        ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions)
+    }
 
     emit:
-    mmi           = MINIMAP2_INDEX.out.index.collect() // channel: [ val(meta), path(mmi) ]
-    fai           = SAMTOOLS_FAIDX.out.fai.collect()   // channel: [ val(meta), path(fai) ]
-    fasta         = ch_fasta                           // channel: [ val(meta), path(fasta) ]
-    vep_resources = untarred_vep                       // channel: [ path(cache) ]
-    versions      = ch_versions                        // channel: [ versions.yml ]
+    mmi             = MINIMAP2_INDEX.out.index.collect()                                   // channel: [ val(meta), path(mmi) ]
+    fai             = SAMTOOLS_FAIDX.out.fai.collect()                                     // channel: [ val(meta), path(fai) ]
+    fasta           = ch_fasta                                                             // channel: [ val(meta), path(fasta) ]
+    vep_resources   = untar_vep_cache ? UNTAR_VEP_CACHE.out.untar.collect() : ch_vep_cache // channel: [ val(meta), path(cache) ]
+    versions        = ch_versions                                                          // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/qc_aligned_reads.nf b/subworkflows/local/qc_aligned_reads.nf
index 2176f807..a7ec0c37 100644
--- a/subworkflows/local/qc_aligned_reads.nf
+++ b/subworkflows/local/qc_aligned_reads.nf
@@ -1,4 +1,5 @@
 include { CRAMINO  } from '../../modules/local/cramino'
+include { FASTQC   } from '../../modules/nf-core/fastqc/main'
 include { MOSDEPTH } from '../../modules/nf-core/mosdepth/main.nf'
 
 workflow QC_ALIGNED_READS {
@@ -11,6 +12,9 @@ workflow QC_ALIGNED_READS {
     main:
     ch_versions = Channel.empty()
 
+    FASTQC ( ch_bam_bai.map { meta, bam, bai -> [ meta, bam ] } )
+    ch_versions = ch_versions.mix(FASTQC.out.versions)
+
     CRAMINO (ch_bam_bai)
     ch_versions = ch_versions.mix(CRAMINO.out.versions)
 
@@ -22,6 +26,7 @@ workflow QC_ALIGNED_READS {
     ch_versions = ch_versions.mix(MOSDEPTH.out.versions)
 
     emit:
+    fastqc_zip           = FASTQC.out.zip           // channel: [ val(meta), path(zip) ]
     mosdepth_summary     = MOSDEPTH.out.summary_txt // channel: [ val(meta), path(txt) ]
     mosdepth_global_dist = MOSDEPTH.out.global_txt  // channel: [ val(meta), path(txt) ]
     mosdepth_region_dist = MOSDEPTH.out.regions_txt // channel: [ val(meta), path(txt) ]
diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf
index c6820e14..97f00869 100644
--- a/subworkflows/local/rank_variants/main.nf
+++ b/subworkflows/local/rank_variants/main.nf
@@ -7,46 +7,49 @@ include { GENMOD_MODELS    } from '../../../modules/nf-core/genmod/models/main'
 include { GENMOD_SCORE     } from '../../../modules/nf-core/genmod/score/main'
 include { GENMOD_COMPOUND  } from '../../../modules/nf-core/genmod/compound/main'
 include { BCFTOOLS_SORT    } from '../../../modules/nf-core/bcftools/sort/main'
-include { TABIX_BGZIP      } from '../../../modules/nf-core/tabix/bgzip/main'
-include { TABIX_TABIX      } from '../../../modules/nf-core/tabix/tabix/main'
 
 workflow RANK_VARIANTS {
 
     take:
-        ch_vcf                // channel: [mandatory] [ val(meta), path(vcf) ]
-        ch_pedfile            // channel: [mandatory] [ path(ped) ]
-        ch_reduced_penetrance // channel: [mandatory] [ path(pentrance) ]
-        ch_score_config       // channel: [mandatory] [ path(ini) ]
+    ch_vcf                       // channel: [mandatory] [ val(meta), path(vcf) ]
+    ch_ped                       // channel: [mandatory] [ val(meta), path(ped) ]
+    ch_genmod_reduced_penetrance // channel: [mandatory] [ val(meta), path(pentrance) ]
+    ch_score_config              // channel: [mandatory] [ val(meta), path(ini) ]
 
     main:
-        ch_versions = Channel.empty()
+    ch_versions = Channel.empty()
 
-        GENMOD_ANNOTATE(ch_vcf)
+    GENMOD_ANNOTATE ( ch_vcf )
+    ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions)
 
-        GENMOD_MODELS(GENMOD_ANNOTATE.out.vcf, ch_pedfile, ch_reduced_penetrance)
+    GENMOD_ANNOTATE.out.vcf
+        .join( ch_ped, failOnMismatch: true )
+        .set { genmod_models_in }
 
-        GENMOD_SCORE(GENMOD_MODELS.out.vcf, ch_pedfile, ch_score_config)
+    GENMOD_MODELS (
+        genmod_models_in,
+        ch_genmod_reduced_penetrance.map { meta, file -> file }
+    )
+    ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions)
 
-        GENMOD_COMPOUND(GENMOD_SCORE.out.vcf)
+    GENMOD_MODELS.out.vcf
+        .join( ch_ped, failOnMismatch: true )
+        .set { genmod_score_in }
 
-        BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf) // SV file needs to be sorted before indexing
+    GENMOD_SCORE (
+        genmod_score_in,
+        ch_score_config.map { meta, file -> file }
+    )
+    ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions)
 
-        TABIX_BGZIP(GENMOD_COMPOUND.out.vcf) //run only for SNVs
+    GENMOD_COMPOUND ( GENMOD_SCORE.out.vcf )
+    ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions)
 
-        ch_vcf = TABIX_BGZIP.out.output.mix(BCFTOOLS_SORT.out.vcf)
-
-        TABIX_TABIX (ch_vcf)
-
-        ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions)
-        ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions)
-        ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions)
-        ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions)
-        ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions)
-        ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions)
-        ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
+    BCFTOOLS_SORT ( GENMOD_COMPOUND.out.vcf )
+    ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions)
 
     emit:
-        vcf      = ch_vcf              // channel: [ val(meta), path(vcf) ]
-        tbi      = TABIX_TABIX.out.tbi // channel: [ val(meta), path(tbi) ]
-        versions = ch_versions         // channel: [ path(versions.yml) ]
+    vcf      = BCFTOOLS_SORT.out.vcf // channel: [ val(meta), path(vcf) ]
+    tbi      = BCFTOOLS_SORT.out.tbi // channel: [ val(meta), path(tbi) ]
+    versions = ch_versions           // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/rank_variants/tests/main.nf.test b/subworkflows/local/rank_variants/tests/main.nf.test
new file mode 100644
index 00000000..f87e18b0
--- /dev/null
+++ b/subworkflows/local/rank_variants/tests/main.nf.test
@@ -0,0 +1,167 @@
+nextflow_workflow {
+
+    name "Test Workflow RANK_VARIANTS"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "RANK_VARIANTS"
+
+    setup {
+        run("PREPARE_GENOME") {
+            script "../../prepare_genome.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'hg38' ],
+                    file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true)
+                ])
+                input[1] = [
+                    [ id: 'vep_cache' ],
+                    file(params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz', checkIfExists:true)
+                ]
+                input[2] = true
+                input[3] = true
+                """
+            }
+        }
+        run("MINIMAP2_ALIGN") {
+            script "../../../../modules/nf-core/minimap2/align/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'project', num_intervals:1 ],
+                    file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true)
+                ]
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = true
+                input[3] = 'csi'
+                input[4] = false
+                input[5] = false
+                """
+            }
+        }
+        run("SHORT_VARIANT_CALLING") {
+            script "../../short_variant_calling/main.nf"
+            process {
+                """
+                input[0] = MINIMAP2_ALIGN.out.bam
+                            .join(MINIMAP2_ALIGN.out.index)
+                            .join(Channel.of([
+                                [ id: 'project', num_intervals:1 ],
+                                file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkIfExists: true)
+                            ]))
+                input[1] = PREPARE_GENOME.out.fasta
+                input[2] = PREPARE_GENOME.out.fai
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+            """
+            }
+        }
+        run("SNV_ANNOTATION") {
+            script "../../snv_annotation/main.nf"
+            process {
+                """
+                input[0] = SHORT_VARIANT_CALLING.out.family_bcf
+                input[1] = [
+                    file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true)
+                ]
+                input[2] = PREPARE_GENOME.out.fasta
+                input[3] = PREPARE_GENOME.out.fai
+                input[4] = PREPARE_GENOME.out.vep_resources.map { meta, cache -> cache }
+                input[5] = Channel.value('110')
+                input[6] = Channel.of([
+                    file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
+                ]).splitCsv(header:true).map { row -> row.vep_files }.collect()
+                input[7] = false
+                input[8] = Channel.value([])
+                input[9] = null
+                input[10] = null
+                """
+            }
+        }
+        run("ANNOTATE_CSQ_PLI") {
+            script "../../../../subworkflows/local/annotate_consequence_pli.nf"
+            process {
+                """
+                input[0] = SNV_ANNOTATION.out.vcf
+                input[1] = [
+                    [ id: 'variant_consequences' ],
+                    [ file(params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+        run("CREATE_PEDIGREE_FILE") {
+            script "../../../../modules/local/create_pedigree_file/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:'project'],
+                    [
+                        [ id: 'project', project: 'project', maternal_id: '0', paternal_id: '0', family_id: 'family', sex: '2', phenotype: '2' ]
+                    ]
+                ]
+                """
+            }
+        }
+    }
+
+    test("1 sample") {
+
+        when {
+            workflow {
+                """
+                input[0] = ANNOTATE_CSQ_PLI.out.vcf.map { meta, vcf -> [ [ id: 'test' ], vcf ] }
+                input[1] = CREATE_PEDIGREE_FILE.out.ped.map { meta, ped -> [ [ id: 'test' ], ped ] }
+                input[2] = Channel.of([
+                    [ id: 'genmod_reduced_penetrance' ],
+                    file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)
+                ])
+                input[3] = Channel.of([
+                    [ id: 'genmod_score_config_snvs' ],
+                    file(params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(
+                    path(workflow.out.vcf.get(0).get(1)).vcf.summary, // Can't snapshot MD5 because VEP output is unstable
+                ).match() }
+            )
+        }
+    }
+
+    test("1 sample - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = ANNOTATE_CSQ_PLI.out.vcf.map { meta, vcf -> [ [ id: 'test' ], vcf ] }
+                input[1] = CREATE_PEDIGREE_FILE.out.ped.map { meta, ped -> [ [ id: 'test' ], ped ] }
+                input[2] = Channel.of([
+                    [ id: 'genmod_reduced_penetrance' ],
+                    file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)
+                ])
+                input[3] = Channel.of([
+                    [ id: 'genmod_score_config_snvs' ],
+                    file(params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.tbi.get(0).get(1).endsWith("tbi") },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/rank_variants/tests/main.nf.test.snap b/subworkflows/local/rank_variants/tests/main.nf.test.snap
new file mode 100644
index 00000000..a955bed6
--- /dev/null
+++ b/subworkflows/local/rank_variants/tests/main.nf.test.snap
@@ -0,0 +1,69 @@
+{
+    "1 sample": {
+        "content": [
+            "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=121, phased=false, phasedAutodetect=false]"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T13:47:43.144635306"
+    },
+    "1 sample - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7089dd9c4bcb1dc87f15d3b1a9d5e89d",
+                    "versions.yml:md5,90ddd1e5113e3c0c61c403c53029d0f1",
+                    "versions.yml:md5,c9446a89a358fa2126b666399c2c804e",
+                    "versions.yml:md5,cc68e7d53d2d24006094e28d37db20a8",
+                    "versions.yml:md5,dd0a9b5a3a16e3bfdcea734de4509dce"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7089dd9c4bcb1dc87f15d3b1a9d5e89d",
+                    "versions.yml:md5,90ddd1e5113e3c0c61c403c53029d0f1",
+                    "versions.yml:md5,c9446a89a358fa2126b666399c2c804e",
+                    "versions.yml:md5,cc68e7d53d2d24006094e28d37db20a8",
+                    "versions.yml:md5,dd0a9b5a3a16e3bfdcea734de4509dce"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-04T14:34:36.22073696"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/rank_variants/tests/nextflow.config b/subworkflows/local/rank_variants/tests/nextflow.config
new file mode 100644
index 00000000..60f0bcf9
--- /dev/null
+++ b/subworkflows/local/rank_variants/tests/nextflow.config
@@ -0,0 +1,122 @@
+process {
+
+    withName: 'PREPARE_GENOME:UNTAR_VEP_CACHE' {
+        ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' }
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
+        ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
+        ext.args = { [
+            '--model_type WGS',
+            "--sample_name=${meta.id}",
+            '-vcf_stats_report=False'
+        ].join(' ') }
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:GLNEXUS' {
+        ext.args = '--config DeepVariant_unfiltered'
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT' {
+        ext.prefix = { "${meta.id}_concat" }
+        ext.args = [
+            '--no-version',
+            '--allow-overlaps'
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_MULTISAMPLE' {
+        ext.prefix = { "${meta.id}_norm_multisample" }
+        ext.args = [
+            '--no-version',
+            '-m -',
+            '--output-type u',
+            '--write-index=csi',
+            '-w 10000'
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_SINGLESAMPLE' {
+        ext.prefix = { "${meta.id}_norm_singlesample" }
+        ext.args = [
+            '--no-version',
+            '-m -',
+            '-w 10000',
+            '--output-type u',
+        ].join(' ')
+    }
+
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
+        ext.prefix = { "${meta.id}_ac" }
+        ext.args = [
+            '--no-version',
+            '--output-type u'
+        ].join(' ')
+    }
+
+    withName: 'SNV_ANNOTATION:BCFTOOLS_FILLTAGS_ANNO' {
+        ext.prefix = { "${meta.id}_filltags_anno" }
+        ext.args = [
+            '--no-version',
+            '--output-type z'
+        ].join(' ')
+    }
+
+    withName: 'MINIMAP2_ALIGN' {
+        ext.args = '-x map-hifi'
+    }
+
+    withName: 'SNV_ANNOTATION:ENSEMBLVEP_SNV' {
+        ext.args = { [
+            "--dir_plugins .",
+            "--plugin LoFtool,LoFtool_scores.txt",
+            "--plugin pLI,pLI_values.txt",
+            '--distance 5000',
+            '--buffer_size 20000',
+            '--format vcf --max_sv_size 248387328',
+            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
+            '--domains --exclude_predicted --force_overwrite',
+            '--hgvs --humdiv --no_progress --numbers',
+            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
+            '--uniprot --vcf',
+            '--no_stats'
+        ].join(' ') }
+    }
+
+    withName: 'ANNOTATE_CSQ_PLI:ADD_MOST_SEVERE_PLI' {
+        ext.prefix = { "${meta.id}_add_most_severe_pli" }
+    }
+
+    withName: 'ANNOTATE_CSQ_PLI:ADD_MOST_SEVERE_CSQ' {
+        ext.prefix = { "${meta.id}_add_most_severe_csq" }
+    }
+
+    withName: 'RANK_VARIANTS:GENMOD_ANNOTATE' {
+        ext.prefix = { "${meta.id}_genmod_annotate" }
+        ext.args = { [
+            '--annotate_regions',
+            '--genome-build 38',
+            '--temp_dir ./'
+            ].join(' ') }
+    }
+
+    withName: 'RANK_VARIANTS:GENMOD_MODELS' {
+        ext.prefix = { "${meta.id}_genmod_models" }
+        ext.args = "--whole_gene --temp_dir ./"
+    }
+
+    withName: 'RANK_VARIANTS:GENMOD_SCORE' {
+        ext.prefix = { "${meta.id}_genmod_score" }
+        ext.args = "--rank_results"
+    }
+
+    withName: 'RANK_VARIANTS:GENMOD_COMPOUND' {
+        ext.prefix = { "${meta.id}_genmod_compound" }
+        ext.args = "--temp_dir ./"
+    }
+
+    withName: 'RANK_VARIANTS:BCFTOOLS_SORT' {
+        ext.prefix = { "${meta.id}_sorted" }
+        ext.args = "--output-type z --write-index=tbi"
+    }
+}
diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap
index 163401f0..6179981a 100644
--- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap
@@ -1,54 +1,65 @@
 {
-    "fai, [], bed, true, 3": {
+    "[], bed, false, true, 3": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "chr22"
                         },
-                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                        "chr22.bed:md5,88ebd3fd77139b3d33af226231eff0df"
                     ]
                 ],
                 "1": [
                     [
-                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
-                        1
+                        "1.bed:md5,37978db9b095a29ebbd64f65dd8f13b3",
+                        2
+                    ],
+                    [
+                        "2.bed:md5,0da4774e61b9c9005122e46f24522604",
+                        2
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
                     "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
-                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240"
                 ],
                 "bed": [
                     [
                         {
-                            "id": "test"
+                            "id": "chr22"
                         },
-                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                        "chr22.bed:md5,88ebd3fd77139b3d33af226231eff0df"
                     ]
                 ],
                 "bed_intervals": [
                     [
-                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
-                        1
+                        "1.bed:md5,37978db9b095a29ebbd64f65dd8f13b3",
+                        2
+                    ],
+                    [
+                        "2.bed:md5,0da4774e61b9c9005122e46f24522604",
+                        2
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
                     "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
-                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240"
                 ]
             },
             [
-                "chr22\t0\t40001"
+                "chr22\t0\t1000",
+                "chr22\t500\t1500",
+                "chr22\t2000\t3000"
             ],
             [
                 [
-                    "chr22\t0\t40001"
+                    "chr22\t0\t1500"
+                ],
+                [
+                    "chr22\t2000\t3000"
                 ]
             ]
         ],
@@ -56,181 +67,178 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-11T13:03:46.414904212"
+        "timestamp": "2024-07-11T13:06:34.382235567"
     },
-    "[], bed, false, false, 3": {
+    "fai, [], bed, true, 3": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "chr22"
+                            "id": {
+                                "id": "test"
+                            }
                         },
-                        "chr22.bed:md5,3b0b598acca89a84aa414e4c95abec1f"
+                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
                 ],
                 "1": [
-                    
+                    [
+                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                        1
+                    ]
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
+                    "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
+                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
                 ],
                 "bed": [
                     [
                         {
-                            "id": "chr22"
+                            "id": {
+                                "id": "test"
+                            }
                         },
-                        "chr22.bed:md5,3b0b598acca89a84aa414e4c95abec1f"
+                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
                 ],
                 "bed_intervals": [
-                    
+                    [
+                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                        1
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
+                    "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
+                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
                 ]
             },
             [
-                "chr22\t0\t1000"
+                "chr22\t0\t40001"
             ],
             [
-                
+                [
+                    "chr22\t0\t40001"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-11T12:53:03.541050122"
+        "timestamp": "2024-10-24T16:45:01.511512303"
     },
-    "[], bed, false, true, 3": {
+    "fai, [], true, true, 3": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "chr22"
+                            "id": {
+                                "id": "test"
+                            }
                         },
-                        "chr22.bed:md5,88ebd3fd77139b3d33af226231eff0df"
+                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
                 ],
                 "1": [
                     [
-                        "1.bed:md5,37978db9b095a29ebbd64f65dd8f13b3",
-                        2
-                    ],
-                    [
-                        "2.bed:md5,0da4774e61b9c9005122e46f24522604",
-                        2
+                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                        1
                     ]
                 ],
                 "2": [
                     "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
                     "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240"
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
+                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
                 ],
                 "bed": [
                     [
                         {
-                            "id": "chr22"
+                            "id": {
+                                "id": "test"
+                            }
                         },
-                        "chr22.bed:md5,88ebd3fd77139b3d33af226231eff0df"
+                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
                 ],
                 "bed_intervals": [
                     [
-                        "1.bed:md5,37978db9b095a29ebbd64f65dd8f13b3",
-                        2
-                    ],
-                    [
-                        "2.bed:md5,0da4774e61b9c9005122e46f24522604",
-                        2
+                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
+                        1
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
                     "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240"
+                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
+                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
                 ]
             },
             [
-                "chr22\t0\t1000",
-                "chr22\t500\t1500",
-                "chr22\t2000\t3000"
+                "chr22\t0\t40001"
             ],
             [
                 [
-                    "chr22\t0\t1500"
-                ],
-                [
-                    "chr22\t2000\t3000"
+                    "chr22\t0\t40001"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-11T13:06:34.382235567"
+        "timestamp": "2024-10-24T16:44:33.772383165"
     },
-    "fai, [], true, true, 3": {
+    "[], bed, false, false, 3": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "chr22"
                         },
-                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                        "chr22.bed:md5,3b0b598acca89a84aa414e4c95abec1f"
                     ]
                 ],
                 "1": [
-                    [
-                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
-                        1
-                    ]
+                    
                 ],
                 "2": [
-                    "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
-                    "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
-                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
+                    
                 ],
                 "bed": [
                     [
                         {
-                            "id": "test"
+                            "id": "chr22"
                         },
-                        "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                        "chr22.bed:md5,3b0b598acca89a84aa414e4c95abec1f"
                     ]
                 ],
                 "bed_intervals": [
-                    [
-                        "1.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
-                        1
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,8174fa0cc1f95ed4b353a948a2cbd4e9",
-                    "versions.yml:md5,beb3374eccd225096e2f7c8ecd3a28be",
-                    "versions.yml:md5,d69b1c1fc4e665c357d541ea3b0a0240",
-                    "versions.yml:md5,e70d387c0dd30530a3e7fe2846ddffe1"
+                    
                 ]
             },
             [
-                "chr22\t0\t40001"
+                "chr22\t0\t1000"
             ],
             [
-                [
-                    "chr22\t0\t40001"
-                ]
+                
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-11T13:03:35.848426979"
+        "timestamp": "2024-07-11T12:53:03.541050122"
     },
     "fai, [], true, false, []": {
         "content": [
@@ -238,7 +246,9 @@
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": {
+                                "id": "test"
+                            }
                         },
                         "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
@@ -252,7 +262,9 @@
                 "bed": [
                     [
                         {
-                            "id": "test"
+                            "id": {
+                                "id": "test"
+                            }
                         },
                         "genome.fasta.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
@@ -272,9 +284,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-11T13:03:25.327078297"
+        "timestamp": "2024-10-24T16:44:24.76494349"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/short_variant_calling/main.nf b/subworkflows/local/short_variant_calling/main.nf
index 5395cd2e..3b743847 100644
--- a/subworkflows/local/short_variant_calling/main.nf
+++ b/subworkflows/local/short_variant_calling/main.nf
@@ -1,11 +1,13 @@
 //
 // Workflow to call and merge SNVs
 //
+include { ADD_FOUND_IN_TAG                            } from '../../../modules/local/add_found_in_tag/main'
 include { BCFTOOLS_CONCAT                             } from '../../../modules/nf-core/bcftools/concat/main'
 include { BCFTOOLS_FILLTAGS                           } from '../../../modules/local/bcftools/filltags/main'
 include { BCFTOOLS_NORM as BCFTOOLS_NORM_MULTISAMPLE  } from '../../../modules/nf-core/bcftools/norm/main'
 include { BCFTOOLS_NORM as BCFTOOLS_NORM_SINGLESAMPLE } from '../../../modules/nf-core/bcftools/norm/main'
-include { DEEPVARIANT                                 } from '../../../modules/nf-core/deepvariant/main'
+include { DEEPVARIANT_RUNDEEPVARIANT                  } from '../../../modules/nf-core/deepvariant/rundeepvariant/main'
+include { DEEPVARIANT_VCFSTATSREPORT                  } from '../../../modules/nf-core/deepvariant/vcfstatsreport/main'
 include { GLNEXUS                                     } from '../../../modules/nf-core/glnexus/main'
 
 workflow SHORT_VARIANT_CALLING {
@@ -27,18 +29,18 @@ workflow SHORT_VARIANT_CALLING {
         }
         .set { ch_deepvariant_in }
 
-    DEEPVARIANT ( ch_deepvariant_in, ch_fasta, ch_fai, [[],[]], ch_par_bed )
-    ch_versions = ch_versions.mix(DEEPVARIANT.out.versions)
+    DEEPVARIANT_RUNDEEPVARIANT ( ch_deepvariant_in, ch_fasta, ch_fai, [[],[]], ch_par_bed )
+    ch_versions = ch_versions.mix(DEEPVARIANT_RUNDEEPVARIANT.out.versions)
 
     // First remove region so we can group per sample
     // Then after grouping remove num_intervals since to match the meta of other workflows
-    DEEPVARIANT.out.vcf
+    DEEPVARIANT_RUNDEEPVARIANT.out.vcf
         .map { meta, vcf ->
             new_meta = meta - meta.subMap('region')
             [ groupKey(new_meta, new_meta.num_intervals ), vcf ]
         }
         .groupTuple()
-        .join( DEEPVARIANT.out.vcf_tbi
+        .join( DEEPVARIANT_RUNDEEPVARIANT.out.vcf_tbi
             .map{ meta, tbi ->
                 new_meta = meta - meta.subMap('region')
                 [ groupKey(new_meta, new_meta.num_intervals ), tbi ]
@@ -59,22 +61,12 @@ workflow SHORT_VARIANT_CALLING {
     BCFTOOLS_NORM_SINGLESAMPLE ( BCFTOOLS_CONCAT.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] }, ch_fasta )
     ch_versions = ch_versions.mix(BCFTOOLS_NORM_SINGLESAMPLE.out.versions)
 
-    // This creates a multisample VCF, with regions from ONE bed file
-    DEEPVARIANT.out.gvcf
+    // This creates one multisample VCF per family, with regions from ONE bed file
+    DEEPVARIANT_RUNDEEPVARIANT.out.gvcf
         .map { meta, gvcf ->
-            [ meta.region.name, meta.project, meta.phenotype == 2, gvcf ]
-        }
-        .groupTuple() // Group all files together per region
-        // If any of the samples in the VCF have an affected phenotype (2)
-        // add this to the meta of the multisample VCF to know if we should run RANK_VARIANTS or not
-        .map { meta, project, affected, gvcfs ->
-            new_meta = [
-                'id': meta,
-                'project': project.first(), // Works only because only one project per run is allowed
-                'contains_affected': affected.any(),
-            ]
-            [ new_meta, gvcfs ]
+            [ [ id:meta.region.name, family_id:meta.family_id ], gvcf ]
         }
+        .groupTuple() // Groups files from the same family together per region
         .set{ glnexus_in }
 
     GLNEXUS( glnexus_in, ch_bed )
@@ -84,17 +76,29 @@ workflow SHORT_VARIANT_CALLING {
     BCFTOOLS_FILLTAGS ( GLNEXUS.out.bcf )
     ch_versions = ch_versions.mix(BCFTOOLS_FILLTAGS.out.versions)
 
-    BCFTOOLS_FILLTAGS.out.vcf
-        .map { meta, vcf -> [ meta, vcf, [] ] }
-        .set { bcftools_norm_in }
+    // Annotate with FOUND_IN tag
+    ADD_FOUND_IN_TAG (
+        BCFTOOLS_FILLTAGS.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        "deepvariant"
+    )
+    ch_versions = ch_versions.mix(ADD_FOUND_IN_TAG.out.versions)
 
     // Decompose and normalize variants
-    BCFTOOLS_NORM_MULTISAMPLE ( bcftools_norm_in, ch_fasta )
+    BCFTOOLS_NORM_MULTISAMPLE (
+        ADD_FOUND_IN_TAG.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] },
+        ch_fasta
+    )
     ch_versions = ch_versions.mix(BCFTOOLS_NORM_MULTISAMPLE.out.versions)
 
+    // This is run before normalization for each sample to mimic run_deepvariant pipeline
+    DEEPVARIANT_VCFSTATSREPORT ( BCFTOOLS_CONCAT.out.vcf )
+    ch_versions = ch_versions.mix(DEEPVARIANT_VCFSTATSREPORT.out.versions)
+
     emit:
-    snp_calls_vcf = BCFTOOLS_NORM_SINGLESAMPLE.out.vcf // channel: [ val(meta), path(bcf) ]
-    combined_bcf  = BCFTOOLS_NORM_MULTISAMPLE.out.vcf  // channel: [ val(meta), path(bcf) ]
-    combined_csi  = BCFTOOLS_NORM_MULTISAMPLE.out.csi  // channel: [ val(meta), path(csi) ]
-    versions      = ch_versions                        // channel: [ path(versions.yml) ]
+    snp_calls_vcf  = BCFTOOLS_NORM_SINGLESAMPLE.out.vcf    // channel: [ val(meta), path(vcf) ]
+    snp_calls_tbi  = BCFTOOLS_NORM_SINGLESAMPLE.out.tbi    // channel: [ val(meta), path(tbi) ]
+    family_bcf     = BCFTOOLS_NORM_MULTISAMPLE.out.vcf     // channel: [ val(meta), path(bcf) ]
+    family_csi     = BCFTOOLS_NORM_MULTISAMPLE.out.csi     // channel: [ val(meta), path(csi) ]
+    vcfstatsreport = DEEPVARIANT_VCFSTATSREPORT.out.report // channel: [ val(meta), path(html) ]
+    versions       = ch_versions                           // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
index d35e9387..04be59dd 100644
--- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
+++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "1 sample - 1 bed, fasta, fai, bed, []": {
+    "1 sample - 1 bed, fasta, fai, [], []": {
         "content": [
             {
                 "0": [
@@ -8,51 +8,80 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,94d38d8fd3c50a7ede72a080fbd4992c"
+                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "genome.bed",
-                            "contains_affected": false
+                            "id": "test",
+                            "single_end": false
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,56d662f0a527803ae72e40625c01014b"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
                     ]
                 ],
                 "2": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
                     ]
                 ],
                 "3": [
+                    [
+                        {
+                            "id": "genome.bed",
+                            "family_id": null
+                        },
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
-                "combined_bcf": [
+                "family_bcf": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,56d662f0a527803ae72e40625c01014b"
+                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
                     ]
                 ],
-                "combined_csi": [
+                "family_csi": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
+                        },
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                    ]
+                ],
+                "snp_calls_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
                     ]
                 ],
                 "snp_calls_vcf": [
@@ -61,26 +90,37 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,94d38d8fd3c50a7ede72a080fbd4992c"
+                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                    ]
+                ],
+                "vcfstatsreport": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T12:18:48.194341252"
+        "timestamp": "2024-11-21T14:31:35.224934094"
     },
-    "2 samples - 2 bed, fasta, fai, bed, [] - stub": {
+    "1 sample - 2 bed, fasta, fai, bed, [] - stub": {
         "content": [
             {
                 "0": [
@@ -89,137 +129,157 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
                     [
                         {
-                            "id": "test2",
+                            "id": "test",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
+                "2": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "2": [
+                "3": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
-                    "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
-                    "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
-                "combined_bcf": [
+                "family_bcf": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "combined_csi": [
+                "family_csi": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "snp_calls_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "snp_calls_vcf": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcfstatsreport": [
                     [
                         {
-                            "id": "test2",
+                            "id": "test",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
-                    "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T12:38:57.50673848"
+        "timestamp": "2024-11-21T14:34:35.379604763"
     },
-    "2 samples - 2 bed, fasta, fai, bed, par_bed - stub": {
+    "1 sample - 1 bed, fasta, fai, bed, []": {
         "content": [
             {
                 "0": [
@@ -228,94 +288,80 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
+                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                    ]
+                ],
+                "1": [
                     [
                         {
-                            "id": "test2",
+                            "id": "test",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
                     ]
                 ],
-                "1": [
+                "2": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
-                        },
-                        "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
                     ]
                 ],
-                "2": [
+                "3": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                    ]
+                ],
+                "4": [
                     [
                         {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "id": "test",
+                            "single_end": false
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
                     ]
                 ],
-                "3": [
+                "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
-                    "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
-                    "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
-                "combined_bcf": [
+                "family_bcf": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ],
-                    [
-                        {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
-                        },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
                     ]
                 ],
-                "combined_csi": [
+                "family_csi": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                    ]
+                ],
+                "snp_calls_tbi": [
                     [
                         {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "id": "test",
+                            "single_end": false
                         },
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@@ -324,41 +370,37 @@
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@@ -367,200 +409,183 @@
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@@ -587,79 +620,209 @@
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@@ -785,94 +1292,113 @@
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@@ -881,41 +1407,42 @@
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@@ -924,202 +1451,207 @@
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+                            "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
-                    "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
-                    "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
-                ],
-                "combined_bcf": [
+                "snp_calls_tbi": [
                     [
                         {
-                            "id": "genome.bed",
-                            "contains_affected": false
+                            "id": "test",
+                            "single_end": false
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,56d662f0a527803ae72e40625c01014b"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
                     ],
                     [
                         {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "id": "test2",
+                            "single_end": false
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,56d662f0a527803ae72e40625c01014b"
+                        "test2_norm_singlesample.vcf.gz.tbi:md5,2c4354a182ae1f4ad94f056b2fbf62a8"
                     ]
                 ],
-                "combined_csi": [
+                "snp_calls_vcf": [
                     [
                         {
-                            "id": "genome.bed",
-                            "contains_affected": false
+                            "id": "test",
+                            "single_end": false
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
                     ],
                     [
                         {
-                            "id": "genome.multi_intervals.bed",
-                            "contains_affected": false
+                            "id": "test2",
+                            "single_end": false
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9"
+                        "test2_norm_singlesample.vcf.gz:md5,0e42833e64e0f427ca09259e17e2765b"
                     ]
                 ],
-                "snp_calls_vcf": [
+                "vcfstatsreport": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,f978f9f75d4892499156218a300fd246"
+                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                    ],
+                    [
+                        {
+                            "id": "test2",
+                            "single_end": false
+                        },
+                        "test2.visual_report.html:md5,3358ec9541a51f43ab77cc79a8ed2f23"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
+                    "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
+                    "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T12:36:53.97901474"
+        "timestamp": "2024-11-21T14:33:13.404225198"
     },
     "1 sample - no bed, fasta, fai, [], [] - stub": {
         "content": [
@@ -1130,85 +1662,125 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     [
                         {
                             "id": [
                                 
                             ],
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "[]_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "2": [
+                "3": [
                     [
                         {
                             "id": [
                                 
                             ],
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "[]_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
-                "combined_bcf": [
+                "family_bcf": [
                     [
                         {
                             "id": [
                                 
                             ],
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "[]_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "combined_csi": [
+                "family_csi": [
                     [
                         {
                             "id": [
                                 
                             ],
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "[]_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "snp_calls_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "snp_calls_vcf": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcfstatsreport": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T12:20:07.024378325"
+        "timestamp": "2024-11-21T14:33:59.832105156"
     },
     "1 sample - 1 bed, fasta, fai, [], [] - stub": {
         "content": [
@@ -1219,76 +1791,116 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "2": [
+                "3": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
-                "combined_bcf": [
+                "family_bcf": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "combined_csi": [
+                "family_csi": [
                     [
                         {
                             "id": "genome.bed",
-                            "contains_affected": false
+                            "family_id": null
                         },
                         "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "snp_calls_tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "snp_calls_vcf": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "vcfstatsreport": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
-                    "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
-                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6"
+                    "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
+                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
+                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
+                    "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T12:20:16.739088461"
+        "timestamp": "2024-11-21T14:34:11.123087909"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/short_variant_calling/tests/nextflow.config b/subworkflows/local/short_variant_calling/tests/nextflow.config
index f9b1d1a5..2b85525c 100644
--- a/subworkflows/local/short_variant_calling/tests/nextflow.config
+++ b/subworkflows/local/short_variant_calling/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    withName: 'DEEPVARIANT' {
+    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
         ext.args = { [
             '--model_type WGS',
@@ -8,11 +8,11 @@ process {
         ].join(' ') }
     }
 
-    withName: 'GLNEXUS' {
+    withName: 'SHORT_VARIANT_CALLING:GLNEXUS' {
         ext.args = '--config DeepVariant_unfiltered'
     }
 
-    withName: 'BCFTOOLS_CONCAT' {
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT' {
         ext.prefix = { "${meta.id}_concat" }
         ext.args = [
             '--no-version',
@@ -20,7 +20,7 @@ process {
         ].join(' ')
     }
 
-    withName: 'BCFTOOLS_NORM_MULTISAMPLE' {
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_MULTISAMPLE' {
         ext.prefix = { "${meta.id}_norm_multisample" }
         ext.args = [
             '--no-version',
@@ -31,17 +31,18 @@ process {
         ].join(' ')
     }
 
-    withName: 'BCFTOOLS_NORM_SINGLESAMPLE' {
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_NORM_SINGLESAMPLE' {
         ext.prefix = { "${meta.id}_norm_singlesample" }
         ext.args = [
             '--no-version',
             '-m -',
             '-w 10000',
-            '--output-type u',
+            '--output-type z',
+            '--write-index=tbi'
         ].join(' ')
     }
 
-    withName: 'BCFTOOLS_FILLTAGS' {
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
         ext.prefix = { "${meta.id}_ac" }
         ext.args = [
             '--no-version',
@@ -49,4 +50,13 @@ process {
         ].join(' ')
     }
 
+    withName: 'SHORT_VARIANT_CALLING:ADD_FOUND_IN_TAG' {
+        ext.prefix = { "${meta.id}_found_in" }
+        ext.args = '--no-version'
+        ext.args2 = [
+            '--output-type z',
+            '--no-version'
+        ].join(' ')
+    }
+
 }
diff --git a/subworkflows/local/snv_annotation/main.nf b/subworkflows/local/snv_annotation/main.nf
index 1bcc22e7..96182294 100644
--- a/subworkflows/local/snv_annotation/main.nf
+++ b/subworkflows/local/snv_annotation/main.nf
@@ -1,23 +1,23 @@
 include { ANNOTATE_CADD                               } from '../annotate_cadd/main'
 include { ECHTVAR_ANNO                                } from '../../../modules/local/echtvar/anno/main'
 include { BCFTOOLS_FILLTAGS as BCFTOOLS_FILLTAGS_ANNO } from '../../../modules/local/bcftools/filltags/main'
-include { ENSEMBLVEP_VEP                              } from '../../../modules/nf-core/ensemblvep/vep/main'
-include { TABIX_TABIX as TABIX_VEP                    } from '../../../modules/nf-core/tabix/tabix/main'
+include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV            } from '../../../modules/nf-core/ensemblvep/vep/main'
+include { TABIX_TABIX as TABIX_ENSEMBLVEP_SNV         } from '../../../modules/nf-core/tabix/tabix/main'
 
 workflow SNV_ANNOTATION {
 
     take:
-    ch_vcf                // channel [mandatory] [ val(meta), path(vcf) ]
-    ch_databases          // channel: [mandatory] [ val(meta), path(db) ]
-    ch_fasta              // channel: [mandatory] [ val(meta), path(fasta) ]
-    ch_fai                // channel: [mandatory] [ val(meta), path(fai) ]
-    ch_vep_cache          // channel: [mandatory] [ path(cache) ]
-    val_vep_cache_version // string: [mandatory] default: 110
-    ch_vep_extra_files    // channel: [mandatory] [ path(files) ]
-    val_annotate_cadd     // bool: [mandatory]
-    ch_cadd_header        // channel: [mandatory] [ path(txt) ]
-    ch_cadd_resources     // channel: [mandatory] [ path(annotation) ]
-    ch_cadd_prescored     // channel: [mandatory] [ path(prescored) ]
+    ch_vcf                   // channel [mandatory] [ val(meta), path(vcf) ]
+    ch_databases             // channel: [mandatory] [ path(db) ]
+    ch_fasta                 // channel: [mandatory] [ val(meta), path(fasta) ]
+    ch_fai                   // channel: [mandatory] [ val(meta), path(fai) ]
+    ch_vep_cache             // channel: [mandatory] [ path(cache) ]
+    val_vep_cache_version    // string: [mandatory] default: 110
+    ch_vep_extra_files       // channel: [mandatory] [ path(files) ]
+    val_annotate_cadd        // bool: [mandatory]
+    ch_cadd_header           // channel: [mandatory] [ path(txt) ]
+    ch_cadd_resources        // channel: [mandatory] [ val(meta), path(annotation) ]
+    ch_cadd_prescored_indels // channel: [mandatory] [ val(meta), path(prescored) ]
 
     main:
     ch_versions = Channel.empty()
@@ -38,7 +38,7 @@ workflow SNV_ANNOTATION {
             BCFTOOLS_FILLTAGS_ANNO.out.tbi,
             ch_cadd_header,
             ch_cadd_resources,
-            ch_cadd_prescored
+            ch_cadd_prescored_indels
         )
         ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions)
 
@@ -53,7 +53,7 @@ workflow SNV_ANNOTATION {
 
     }
 
-    ENSEMBLVEP_VEP (
+    ENSEMBLVEP_SNV (
         ch_vep_in,
         "GRCh38",
         "homo_sapiens",
@@ -62,13 +62,13 @@ workflow SNV_ANNOTATION {
         ch_fasta,
         ch_vep_extra_files
     )
-    ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions)
+    ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions)
 
-    TABIX_VEP ( ENSEMBLVEP_VEP.out.vcf )
-    ch_versions = ch_versions.mix(TABIX_VEP.out.versions)
+    TABIX_ENSEMBLVEP_SNV ( ENSEMBLVEP_SNV.out.vcf )
+    ch_versions = ch_versions.mix(TABIX_ENSEMBLVEP_SNV.out.versions)
 
     emit:
-    vcf      = ENSEMBLVEP_VEP.out.vcf
-    tbi      = TABIX_VEP.out.tbi
+    vcf      = ENSEMBLVEP_SNV.out.vcf
+    tbi      = TABIX_ENSEMBLVEP_SNV.out.tbi
     versions = ch_versions
 }
diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test b/subworkflows/local/snv_annotation/tests/main.nf.test
index 0d288ccb..6cf9e390 100644
--- a/subworkflows/local/snv_annotation/tests/main.nf.test
+++ b/subworkflows/local/snv_annotation/tests/main.nf.test
@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../"
     workflow "SNV_ANNOTATION"
     config "./nextflow.config"
-    tag "SNV_ANNOTATION"
 
     setup {
         run("GUNZIP") {
@@ -83,17 +82,17 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = SHORT_VARIANT_CALLING.out.combined_bcf
+                input[0] = SHORT_VARIANT_CALLING.out.family_bcf
                 input[1] = [
                     file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true)
                 ]
                 input[2] = GUNZIP.out.gunzip
                 input[3] = SAMTOOLS_FAIDX.out.fai
-                input[4] = UNTAR.out.untar.map { meta, cache -> cache }
+                input[4] = UNTAR.out.untar.map { meta, cache -> cache}
                 input[5] = Channel.value('110')
-                input[6] = [
+                input[6] = Channel.of([
                     file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
-                ]
+                ]).splitCsv(header:true).map { row -> row.vep_files }.collect()
                 input[7] = false
                 input[8] = Channel.value([])
                 input[9] = null
@@ -108,8 +107,8 @@ nextflow_workflow {
                 { assert snapshot(
                     workflow.out.versions,
                     file(workflow.out.tbi.get(0).get(1)).name,
-                    path(workflow.out.vcf.get(0).get(1)).linesGzip[48..118], // Stable
-                    path(workflow.out.vcf.get(0).get(1)).linesGzip[121..150] // Stable
+                    path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    path(workflow.out.vcf.get(0).get(1)).vcf.summary,
                 ).match() }
             )
         }
@@ -125,7 +124,7 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0] = SHORT_VARIANT_CALLING.out.combined_bcf
+                input[0] = SHORT_VARIANT_CALLING.out.family_bcf
                 input[1] = [
                     file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true)
                 ]
@@ -133,9 +132,9 @@ nextflow_workflow {
                 input[3] = SAMTOOLS_FAIDX.out.fai
                 input[4] = UNTAR.out.untar.map { meta, cache -> cache }
                 input[5] = Channel.value('110')
-                input[6] = [
+                input[6] = Channel.of([
                     file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true)
-                ]
+                ]).splitCsv(header:true).map { row -> row.vep_files }.collect()
                 input[7] = false
                 input[8] = Channel.value([])
                 input[9] = null
diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap
index f491df0c..2973a379 100644
--- a/subworkflows/local/snv_annotation/tests/main.nf.test.snap
+++ b/subworkflows/local/snv_annotation/tests/main.nf.test.snap
@@ -2,16 +2,16 @@
     "bcf, db, vep_cache, '110', -stub": {
         "content": [
             [
+                "versions.yml:md5,1c67249781a135b3abbc3c7e63af4d0b",
                 "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22",
-                "versions.yml:md5,992301857689684643c42695c032a7f2",
-                "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c",
-                "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533"
+                "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533",
+                "versions.yml:md5,f533675b4401f25d7dcfc9f63abeb619"
             ],
             [
                 [
                     {
                         "id": "test_data.bed",
-                        "contains_affected": false
+                        "family_id": null
                     },
                     "test_data.bed.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
@@ -20,137 +20,34 @@
                 [
                     {
                         "id": "test_data.bed",
-                        "contains_affected": false
+                        "family_id": null
                     },
                     "test_data.bed.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-12T10:11:15.912554747"
+        "timestamp": "2024-11-12T17:30:08.202090846"
     },
     "bcf, db, vep_cache, '110'": {
         "content": [
             [
+                "versions.yml:md5,1c67249781a135b3abbc3c7e63af4d0b",
                 "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22",
-                "versions.yml:md5,992301857689684643c42695c032a7f2",
-                "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c",
-                "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533"
+                "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533",
+                "versions.yml:md5,f533675b4401f25d7dcfc9f63abeb619"
             ],
             "test_data.bed.vcf.gz.tbi",
-            [
-                "##INFO=<ID=CSQ,Number=.,Type=String,Description=\"Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID\">",
-                "##VEP-command-line='vep --assembly GRCh38 --cache --cache_version 110 --compress_output bgzip --database 0 --dir_cache [PATH]/vep_cache --fasta hg38.test.fa --fork 2 --input_file test_data.bed_filltags_anno.vcf.gz --offline --output_file test_data.bed.vcf.gz --vcf'",
-                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest",
-                "chr16\t63972\tchr16_63972_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000262316|protein_coding||3/17||||||||||-1||HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000417043|nonsense_mediated_decay||2/3||||||||||-1||HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000419764|protein_coding||3/3||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000428730|nonsense_mediated_decay||2/16||||||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000448893|protein_coding|||||||||||4210|-1|cds_start_NF|HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000450643|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|downstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000472390|retained_intron|||||||||||580|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000482904|retained_intron|||||||||||1766|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000486045|retained_intron|||||||||||3779|-1||HGNC|HGNC:20561,C|non_coding_transcript_exon_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000487201|retained_intron|2/3||||1177|||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000493647|retained_intron|||||||||||3292|-1||HGNC|HGNC:20561\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:11:20,11,0:..",
-                "chr16\t86889\tchr16_86889_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000219431|protein_coding|||||||||||1047|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000356432|protein_coding|||||||||||1043|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000397817|protein_coding|||||||||||1038|1||HGNC|HGNC:7211,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000399953|protein_coding||11/11||||||||||-1||HGNC|HGNC:14124,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000436333|protein_coding|||||||||||1205|1|cds_end_NF|HGNC|HGNC:7211,C|upstream_gene_variant|MODIFIER||ENSG00000269482|Transcript|ENST00000601483|lncRNA|||||||||||3742|1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000610509|retained_intron||1/2||||||||||-1||HGNC|HGNC:14124,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000611875|protein_coding||13/13||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000621703|nonsense_mediated_decay||10/10||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000622194|nonsense_mediated_decay||11/11||||||||||-1||HGNC|HGNC:14124\tGT:DP:AD:GQ:PL:RNC\t1/1:28:0,28:18:21,20,0:..",
-                "chr16\t160055\tchr16_160055_C_G\tC\tG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3067|1||HGNC|HGNC:4836,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4427|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:17:18,22,0:..",
-                "chr16\t160070\tchr16_160070_C_CGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\tC\tCGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3051|1||HGNC|HGNC:4836,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4411|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:8,7:2:9,0,18:..",
-                "chr16\t160089\tchr16_160089_TG_T\tTG\tT\t14\t.\tAF=0.5;AQ=14;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3032|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4392|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:25,5:15:14,0,29:..",
-                "chr16\t160180\tchr16_160180_C_T\tC\tT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2942|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4302|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:1,28:15:15,25,0:..",
-                "chr16\t160216\tchr16_160216_T_A\tT\tA\t10\t.\tAF=1;AQ=10;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2906|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4266|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,27:6:10,6,0:..",
-                "chr16\t160217\tchr16_160217_C_T\tC\tT\t9\t.\tAF=1;AQ=9;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2905|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4265|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:27:0,27:5:9,3,0:..",
-                "chr16\t160326\tchr16_160326_T_A\tT\tA\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2796|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4156|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:14:15,18,0:..",
-                "chr16\t160327\tchr16_160327_C_T\tC\tT\t16\t.\tAF=1;AQ=16;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2795|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4155|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:3,26:14:16,17,0:..",
-                "chr16\t160388\tchr16_160388_G_GGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\tG\tGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t15\t.\tAF=0.5;AQ=15;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2733|1||HGNC|HGNC:4836,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4093|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:31:4,14:11:15,0,12:..",
-                "chr16\t160728\tchr16_160728_C_T\tC\tT\t5\t.\tAF=1;AQ=5;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2394|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3754|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:8,22:4:5,3,0:..",
-                "chr16\t160746\tchr16_160746_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2376|1||HGNC|HGNC:4836,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3736|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:23,7:10:10,0,18:..",
-                "chr16\t160751\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tAG\tA\t8\t.\tAF=0.5;AQ=8;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2370|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3730|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/0:22:.,7:6:0,0,0:..",
-                "chr16\t160752\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tG\tGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\t8\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2369|1||HGNC|HGNC:4836,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3729|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:.,14:6:0,0,0:..",
-                "chr16\t161210\tchr16_161210_GC_G\tGC\tG\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1911|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4767|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3271|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:27:21,5:7:6,0,27:..",
-                "chr16\t161474\tchr16_161474_TA_T\tTA\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1647|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4503|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3007|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:25:16,9:23:22,0,39:..",
-                "chr16\t162329\tchr16_162329_G_A\tG\tA\t23\t.\tAF=0.5;AQ=23;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||793|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3649|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2153|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:24:23,0,41:..",
-                "chr16\t162650\tchr16_162650_C_T\tC\tT\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||472|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3328|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1832|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:24:9,15:33:34,0,41:..",
-                "chr16\t163106\tchr16_163106_C_T\tC\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||16|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2872|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1376|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:22:22,0,39:..",
-                "chr16\t163140\tchr16_163140_T_G\tT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||19|||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2838|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1342|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:17,0,39:..",
-                "chr16\t163143\tchr16_163143_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||22|||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2835|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1339|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:16,0,41:..",
-                "chr16\t163229\tchr16_163229_T_C\tT\tC\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2749|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1253|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:3:0,0,27:..",
-                "chr16\t163796\tchr16_163796_T_A\tT\tA\t12\t.\tAF=1;AQ=12;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2182|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4883|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||686|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:15:0,15:7:12,7,0:..",
-                "chr16\t163800\tchr16_163800_G_A\tG\tA\t8\t.\tAF=1;AQ=8;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2178|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4879|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||682|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:16:2,14:3:8,0,0:..",
-                "chr16\t163804\tchr16_163804_G_A\tG\tA\t14\t.\tAF=1;AQ=14;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2174|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4875|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||678|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:13:14,16,0:..",
-                "chr16\t164431\tchr16_164431_T_TG\tT\tTG\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1546|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4247|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||50|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:22:25,25,0:..",
-                "chr16\t164541\tchr16_164541_G_GGTCC\tG\tGGTCC\t26\t.\tAF=0.5;AQ=26;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GTCC|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|2/3||||155-156|||||||1||HGNC|HGNC:4836,GTCC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1436|1||HGNC|HGNC:4826,GTCC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4137|1||HGNC|HGNC:4825,GTCC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GTCC|non_coding_transcript_exon_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|1/3||||60-61|||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,7:26:26,0,39:..",
-                "chr16\t164690\tchr16_164690_C_CGCGGGGCGCGGTGCGGGCGGG\tC\tCGCGGGGCGCGGTGCGGGCGGG\t27\t.\tAF=0.5;AQ=27;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1287|1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3988|1||HGNC|HGNC:4825,GCGGGGCGCGGTGCGGGCGGG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,14:25:27,0,28:..",
-                "chr16\t164723\tchr16_164723_C_T\tC\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1255|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3956|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:15,4:11:11,0,21:..",
-                "chr16\t164731\tchr16_164731_C_CG\tC\tCG\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:2,14:2:14,0,22:..",
-                "chr16\t164740\tchr16_164740_C_T\tC\tT\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1238|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3939|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:1,18:2:2,0,1:..",
-                "chr16\t164771\tchr16_164771_T_C\tT\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1207|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3908|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,6:4:10,0,25:..",
-                "chr16\t164791\tchr16_164791_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1187|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3888|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,15:15:16,0,20:..",
-                "chr16\t164800\tchr16_164800_G_GGCGGGGTCGCGGGGCGGGGCGAGGTC\tG\tGGCGGGGTCGCGGGGCGGGGCGAGGTC\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1177|1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3878|1||HGNC|HGNC:4825,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,4:5:4,0,19:..",
-                "chr16\t164817\tchr16_164817_C_A\tC\tA\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1161|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3862|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:8,13:21:22,0,27:..",
-                "chr16\t164831\tchr16_164831_C_CG\tC\tCG\t4\t.\tAF=1;AQ=4;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1146|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3847|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:4,15:2:4,0,0:..",
-                "chr16\t164839\tchr16_164839_G_GGT\tG\tGGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1138|1||HGNC|HGNC:4826,GT|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3839|1||HGNC|HGNC:4825,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:2,15:10:15,10,0:..",
-                "chr16\t164871\tchr16_164871_T_G\tT\tG\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1107|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3808|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,7:14:13,0,33:..",
-                "chr16\t164884\tchr16_164884_G_GT\tG\tGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1093|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3794|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:15:15,22,0:..",
-                "chr16\t164892\tchr16_164892_CG_C\tCG\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1085|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3786|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:2,0,21:..",
-                "chr16\t164907\tchr16_164907_C_A\tC\tA\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1071|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3772|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,8:5:3,0,20:..",
-                "chr16\t164931\tchr16_164931_C_G\tC\tG\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1047|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3748|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:1,8:5:3,0,19:..",
-                "chr16\t164932\tchr16_164932_G_GGGCGGGC\tG\tGGGCGGGC\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGCGGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1045|1||HGNC|HGNC:4826,GGCGGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3746|1||HGNC|HGNC:4825,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:2,7:4:1,0,15:..",
-                "chr16\t164942\tchr16_164942_G_GT\tG\tGT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1035|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3736|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:0,8:6:4,0,14:..",
-                "chr16\t164953\tchr16_164953_G_GGCGGC\tG\tGGCGGC\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1024|1||HGNC|HGNC:4826,GCGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3725|1||HGNC|HGNC:4825,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:13:13,0,33:..",
-                "chr16\t164985\tchr16_164985_C_CG\tC\tCG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||992|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3693|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:19:1,18:16:18,18,0:..",
-                "chr16\t165212\tchr16_165212_TC_T\tTC\tT\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||57|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||765|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3466|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:3,0,30:..",
-                "chr16\t165380\tchr16_165380_G_A\tG\tA\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||224|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||598|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3299|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,43:..",
-                "chr16\t165856\tchr16_165856_G_C\tG\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||700|1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||122|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2823|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,44:..",
-                "chr16\t166191\tchr16_166191_C_CG\tC\tCG\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1035|1||HGNC|HGNC:4836,G|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2487|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,6:23:22,0,36:..",
-                "chr16\t166518\tchr16_166518_TG_T\tTG\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1363|1||HGNC|HGNC:4836,-|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||2/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2160|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:16,4:12:11,0,32:..",
-                "chr16\t167928\tchr16_167928_GT_G\tGT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4947|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2773|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1165|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4961|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||750|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4965|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:17:17,0,31:..",
-                "chr16\t167947\tchr16_167947_T_TC\tT\tTC\t19\t.\tAF=0.5;AQ=19;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2791|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1183|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:11,10:18:19,0,22:..",
-                "chr16\t167948\tchr16_167948_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2792|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1184|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:10,10:10:10,0,17:..",
-                "chr16\t168533\tchr16_168533_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4343|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3377|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1769|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4357|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||146|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4361|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4411|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4969|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:29:29,0,43:..",
-                "chr16\t168736\tchr16_168736_A_G\tA\tG\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4140|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3580|1||HGNC|HGNC:4836,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1972|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4154|1||HGNC|HGNC:4824,G|non_coding_transcript_exon_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|1/3||||58|||||||1||HGNC|HGNC:4825,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4158|1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4208|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4766|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:34:34,0,48:..",
-                "chr16\t169117\tchr16_169117_TG_T\tTG\tT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3758|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3962|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2354|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3772|1||HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3776|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3826|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4384|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:17,3:6:4,0,27:..",
-                "chr16\t169404\tchr16_169404_TC_T\tTC\tT\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3471|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4249|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2641|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3485|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||71|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3489|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3539|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4097|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,2:7:5,0,30:..",
-                "chr16\t169624\tchr16_169624_TC_T\tTC\tT\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3251|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4469|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2861|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3265|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||291|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3269|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3319|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3877|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:11:10,0,32:..",
-                "chr16\t170831\tchr16_170831_T_TCACA\tT\tTCACA\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2044|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4067|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2058|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1497|1||HGNC|HGNC:4825,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2062|1||HGNC|HGNC:4824,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2112|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2670|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:6,6:3:19,0,25:..",
-                "chr16\t170862\tchr16_170862_C_CACACA\tC\tCACACA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2013|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4098|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2027|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1528|1||HGNC|HGNC:4825,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2031|1||HGNC|HGNC:4824,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2081|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2639|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,2:7:5,0,28:..",
-                "chr16\t170943\tchr16_170943_AG_A\tAG\tA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1932|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4180|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1946|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1610|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1950|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2000|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2558|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:18,2:4:1,0,26:..",
-                "chr16\t171206\tchr16_171206_T_TTTA\tT\tTTTA\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4442|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1683|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1872|1||HGNC|HGNC:4825,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1687|1||HGNC|HGNC:4824,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1737|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2295|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:13:13,0,22:..",
-                "chr16\t171219\tchr16_171219_T_TTA\tT\tTTA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1656|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4455|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1670|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1885|1||HGNC|HGNC:4825,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1674|1||HGNC|HGNC:4824,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1724|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2282|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,3:4:1,0,20:..",
-                "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t9\t.\tAF=0.5;AQ=9;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1655|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4456|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1886|1||HGNC|HGNC:4825,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1673|1||HGNC|HGNC:4824,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1723|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2281|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:10:9,0,23:..",
-                "chr16\t171534\tchr16_171534_AT_A\tAT\tA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1341|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4771|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1355|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2201|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1359|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1409|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1967|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,5:20:20,0,40:..",
-                "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t21\t.\tAF=0.5;AQ=21;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||994|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4798|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4822|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1008|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2548|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4816|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1012|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1062|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4866|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1620|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:21:21,0,35:.."
-            ],
-            [
-                "chr16\t172418\tchr16_172418_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||458|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4262|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4286|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||472|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3084|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4280|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||476|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||526|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4330|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4895|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1084|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:16:20,17,0:..",
-                "chr16\t172636\tchr16_172636_C_T\tC\tT\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||240|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4044|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4068|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||254|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3302|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4062|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||258|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||308|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4112|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4677|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||866|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:1,17:14:23,14,0:..",
-                "chr16\t172870\tchr16_172870_G_C\tG\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||6|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3810|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3834|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||20|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3536|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3828|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||24|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||74|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3878|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4443|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||632|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:20:24,22,0:..",
-                "chr16\t173116\tchr16_173116_TC_T\tTC\tT\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3563|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3587|1||HGNC|HGNC:4823,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3783|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3581|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|1/2||||224|||||||1||HGNC|HGNC:4824,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding||1/1||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3631|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4196|-1|||,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||385|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,3:8:6,0,30:..",
-                "chr16\t173707\tchr16_173707_A_G\tA\tG\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=0.19;cadd_phred=3.05;CSQ=G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|3/3||||573|||||||1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||2973|1||HGNC|HGNC:4823,G|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||4847|1||RFAM|,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||2997|1||HGNC|HGNC:4823,G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|3/3||||510|||||||1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4373|1||HGNC|HGNC:4825,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||2991|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||32|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||244|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3041|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||3606|-1|||,G|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||47|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:25:27,27,0:..",
-                "chr16\t176848\tchr16_176848_GC_G\tGC\tG\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3610|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1705|1||RFAM|,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||152|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3174|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3386|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron||1/1||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||464|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3189|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:6:5,0,28:..",
-                "chr16\t176953\tchr16_176953_CA_C\tCA\tC\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3505|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|2/3||||158|121|41|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1600|1||RFAM|,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|2/3||||85|25|9|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||257|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3279|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3491|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|2/2||||90|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||359|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3294|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:7:5,0,30:..",
-                "chr16\t177485\tchr16_177485_AC_A\tAC\tA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||2973|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|3/3||||541|||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1068|1||RFAM|,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|3/3||||468|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|2/2||||640|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3811|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4023|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||212|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|1/1||||5|||||||-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3826|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:13,4:6:5,0,31:..",
-                "chr16\t274052\tchr16_274052_A_G\tA\tG\t28\t.\tAF=1;AQ=28;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant&NMD_transcript_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000168869|nonsense_mediated_decay|5/15||||353|250|84|L|Tta/Cta|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000301679|protein_coding|||||||||||3972|1||HGNC|HGNC:14163,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000316163|protein_coding|6/17||||434|357|119|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000359740|protein_coding|5/16||||387|387|129|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000397770|protein_coding|6/17||||453|420|140|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000472466|retained_intron|||||||||||887|-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000477143|retained_intron|1/9||||905|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000481672|retained_intron|2/11||||110|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000493449|retained_intron|5/9||||1199|||||||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000600536|nonsense_mediated_decay|||||||||||4109|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000653392|nonsense_mediated_decay|||||||||||4216|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000654053|nonsense_mediated_decay|||||||||||4154|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000659283|nonsense_mediated_decay|||||||||||1869|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000666018|nonsense_mediated_decay|||||||||||4097|1||HGNC|HGNC:14163\tGT:DP:AD:GQ:PL:RNC\t1/1:32:0,32:26:28,29,0:..",
-                "chr16\t286660\tchr16_286660_G_A\tG\tA\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000219406|protein_coding|9/11||||1353|1347|449|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000219409|protein_coding|||||||||||3650|1||HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|||||||||||781|-1||HGNC|HGNC:903,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000404312|protein_coding|9/11||||1343|1338|446|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000414650|protein_coding|||||||||||3850|1|cds_end_NF|HGNC|HGNC:680,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000435833|protein_coding|3/5||||234|234|78|T|acG/acA|||1|cds_start_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000447871|protein_coding|||||||||||3972|1|cds_end_NF|HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000456379|protein_coding|||||||||||1520|1|cds_start_NF&cds_end_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000457798|protein_coding|||||||||||1530|-1|cds_start_NF|HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000462950|protein_coding_CDS_not_defined|||||||||||1084|1||HGNC|HGNC:14180,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000467212|retained_intron|8/10||||1418|||||||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000477621|retained_intron|||||||||||3820|1||HGNC|HGNC:680,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000482665|retained_intron|5/7||||1630|||||||1||HGNC|HGNC:14180\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:19:25,19,0:..",
-                "chr16\t309953\tchr16_309953_A_G\tA\tG\t33\t.\tAF=0.5;AQ=33;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding||4/10||||||||||-1||HGNC|HGNC:903,G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding||4/9||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron||3/7||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||3/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:11:6,5:33:33,0,44:..",
-                "chr16\t346264\tchr16_346264_A_G\tA\tG\t31\t.\tAF=0.5;AQ=31;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|2/11||||1198|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|2/10||||924|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|non_coding_transcript_exon_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|1/8||||59|||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||1/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:26:15,11:31:31,0,40:..",
-                "chr16\t377013\tchr16_377013_G_C\tG\tC\t28\t.\tAF=0.5;AQ=28;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000250930|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000424078|protein_coding|||||||||||2162|-1|cds_start_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000427313|protein_coding||4/4||||||||||-1|cds_end_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000431232|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000448854|protein_coding|||||||||||1798|-1|cds_start_NF|HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000467452|retained_intron|||||||||||1938|-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000475348|retained_intron|||||||||||538|-1||HGNC|HGNC:17205,C|downstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000476735|protein_coding_CDS_not_defined|||||||||||95|-1||HGNC|HGNC:17205\tGT:DP:AD:GQ:PL:RNC\t0/1:17:11,6:29:28,0,42:..",
-                "chr16\t520623\tchr16_520623_G_A\tG\tA\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000262305|protein_coding||13/13||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000434585|protein_coding||14/14||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000450428|protein_coding||11/11||||||||||1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000461009|retained_intron|||||||||||1515|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000464263|retained_intron|||||||||||861|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000487899|retained_intron|||||||||||1605|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|LINC00235|ENSG00000277142|Transcript|ENST00000622160|lncRNA|||||||||||4532|-1||HGNC|HGNC:14138\tGT:DP:AD:GQ:PL:RNC\t0/1:18:9,9:34:34,0,44:..",
-                "chr16\t551632\tchr16_551632_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|CAPN15|ENSG00000103326|Transcript|ENST00000219611|protein_coding|9/14||||2820|2313|771|G|ggT/ggC|||1||HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000562370|protein_coding|||||||||||4240|1|cds_end_NF|HGNC|HGNC:11182,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000565010|retained_intron|||||||||||665|1||HGNC|HGNC:11182,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261691|Transcript|ENST00000565879|lncRNA||1/1||||||||||-1|||,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000566977|protein_coding|||||||||||1123|1|cds_start_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000568988|protein_coding|||||||||||3423|1|cds_end_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000637507|protein_coding|||||||||||3601|1|cds_end_NF|HGNC|HGNC:11182\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:15:21,16,0:..",
-                "chr16\t582180\tchr16_582180_G_C\tG\tC\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000026218|protein_coding||9/9||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000321878|protein_coding||9/10||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000409527|protein_coding||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000420990|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000422307|protein_coding|||||||||||4946|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000443147|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000470411|protein_coding|||||||||||4963|1||HGNC|HGNC:14135,C|non_coding_transcript_exon_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000476438|retained_intron|1/2||||420|||||||1||HGNC|HGNC:14135,C|intron_variant&non_coding_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000480424|retained_intron||3/4||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000537901|retained_intron|||||||||||3378|1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540241|protein_coding||2/3||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540548|protein_coding_CDS_not_defined|||||||||||310|1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000544860|protein_coding_CDS_not_defined|||||||||||3337|1||HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000634341|retained_intron|||||||||||697|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635205|nonsense_mediated_decay||3/4||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635909|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635935|protein_coding_CDS_not_defined|||||||||||1403|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636005|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636657|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000637468|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638143|nonsense_mediated_decay|||||||||||1258|1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638152|protein_coding_CDS_not_defined|||||||||||1404|1||HGNC|HGNC:14135\tGT:DP:AD:GQ:PL:RNC\t1/1:6:0,6:9:25,8,0:..",
-                "chr16\t627629\tchr16_627629_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000248139|protein_coding|6/6||||1079|||||||1||HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||3356|1||HGNC|HGNC:30912,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000509637|nonsense_mediated_decay|||||||||||1636|1|cds_start_NF|HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000535977|protein_coding|7/7||||1075|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000538492|protein_coding|7/7||||927|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000539661|protein_coding|7/7||||967|||||||1||HGNC|HGNC:18285,C|non_coding_transcript_exon_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000561781|retained_intron|2/2||||796|||||||1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000563109|protein_coding|||||||||||46|1|cds_start_NF&cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000564703|protein_coding|||||||||||1512|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000565511|nonsense_mediated_decay|||||||||||1546|1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000566290|protein_coding|||||||||||214|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000568586|protein_coding|||||||||||1508|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000569575|protein_coding|||||||||||1603|1|cds_end_NF|HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||1610|1||HGNC|HGNC:30912\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:13:20,13,0:..",
-                "chr16\t638557\tchr16_638557_A_C\tA\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000301686|protein_coding|||||||||||2252|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000307650|protein_coding|||||||||||3271|1||HGNC|HGNC:14142,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||4440|1||HGNC|HGNC:30912,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000338401|protein_coding|||||||||||2215|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397664|protein_coding|||||||||||2206|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397665|protein_coding|||||||||||2267|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397666|protein_coding|||||||||||2255|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000448973|retained_intron|||||||||||2247|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000456420|nonsense_mediated_decay|||||||||||2318|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000474840|nonsense_mediated_decay|||||||||||3372|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000491999|nonsense_mediated_decay|||||||||||3289|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000564039|nonsense_mediated_decay|||||||||||2279|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565163|protein_coding|||||||||||2297|-1|cds_start_NF&cds_end_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565799|retained_intron|||||||||||2290|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568077|nonsense_mediated_decay|||||||||||2226|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568773|protein_coding|||||||||||2322|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568830|protein_coding|||||||||||2199|-1|cds_end_NF|HGNC|HGNC:14141,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||4441|1||HGNC|HGNC:30912,C|intron_variant&non_coding_transcript_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000611328|protein_coding_CDS_not_defined||1/3||||||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000614890|protein_coding|||||||||||2191|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000615744|protein_coding_CDS_not_defined|||||||||||3894|1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619114|protein_coding_CDS_not_defined|2/2||||576|||||||1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619377|protein_coding_CDS_not_defined|2/2||||664|||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000620462|retained_intron|||||||||||3926|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000629534|protein_coding|||||||||||3292|1||HGNC|HGNC:14142\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:24,17,0:..",
-                "chr16\t655844\tchr16_655844_T_C\tT\tC\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|17/41||||1973|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000420061|retained_intron|17/17||||1985|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|3/20||||614|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|||||||||||431|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548844|protein_coding_CDS_not_defined|||||||||||2716|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548859|retained_intron|||||||||||589|1||HGNC|HGNC:26960,C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|17/41||||2013|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549648|retained_intron|17/17||||1988|||||||1||HGNC|HGNC:26960,C|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550593|retained_intron|||||||||||2374|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550739|protein_coding|||||||||||3401|1|cds_start_NF&cds_end_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552648|protein_coding_CDS_not_defined|4/7||||455|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||2014|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|||||||||||577|1|cds_start_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552943|retained_intron|15/26||||3591|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER||ENSG00000262528|Transcript|ENST00000573609|lncRNA|1/2||||351|||||||-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:23,17,0:..",
-                "chr16\t667523\tchr16_667523_G_T\tG\tT\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|41/41||||5233|5181|1727|P|ccG/ccT|||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000315082|protein_coding|||||||||||609|1||HGNC|HGNC:21169,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000315764|protein_coding|6/6||||1147|834|278|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|||||||||||4090|1||HGNC|HGNC:26960,T|missense_variant|MODERATE|WDR90|ENSG00000161996|Transcript|ENST00000546896|protein_coding|2/2||||89|89|30|R/L|cGt/cTt|||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546923|retained_intron|||||||||||4787|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|24/24||||3541|||||||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547543|protein_coding_CDS_not_defined|||||||||||778|1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000547944|protein_coding|7/7||||1365|978|326|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548448|retained_intron|||||||||||1162|1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548603|protein_coding_CDS_not_defined|||||||||||4086|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549024|retained_intron|12/12||||1951|||||||1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|41/41||||5279|5187|1729|P|ccG/ccT|||1||HGNC|HGNC:26960,T|3_prime_UTR_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000551100|protein_coding|3/3||||315|||||||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||4085|1||HGNC|HGNC:26960,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|22/22||||2826|||||||1|cds_start_NF|HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000553080|retained_intron|6/6||||1635|||||||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561711|retained_intron|||||||||||4394|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561929|protein_coding|||||||||||686|1|cds_start_NF&cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561983|nonsense_mediated_decay|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562333|nonsense_mediated_decay|||||||||||664|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562598|retained_intron|||||||||||659|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562708|retained_intron|||||||||||589|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563134|protein_coding|||||||||||583|1|cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563637|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563776|retained_intron|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000565004|retained_intron|||||||||||3559|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566214|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566965|retained_intron|||||||||||1037|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567017|retained_intron|||||||||||639|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567589|retained_intron|||||||||||3005|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568636|retained_intron|||||||||||1135|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568950|retained_intron|||||||||||655|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569358|retained_intron|||||||||||2932|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569675|retained_intron|||||||||||612|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569706|retained_intron|||||||||||609|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569943|protein_coding_CDS_not_defined|||||||||||830|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570092|retained_intron|||||||||||601|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570280|nonsense_mediated_decay|||||||||||630|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000602564|retained_intron|||||||||||657|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000697194|protein_coding|||||||||||577|1||HGNC|HGNC:21169\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:23:27,24,0:..",
-                "chr16\t690466\tchr16_690466_A_G\tA\tG\t26\t.\tAF=1;AQ=26;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000248142|protein_coding|||||||||||22|-1||HGNC|HGNC:20852,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000293883|protein_coding|||||||||||68|-1||HGNC|HGNC:20852,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000397621|protein_coding|||||||||||2034|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562563|protein_coding|||||||||||2461|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562585|protein_coding_CDS_not_defined|||||||||||4192|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562648|retained_intron|||||||||||2032|-1||HGNC|HGNC:14150,G|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000566927|lncRNA||1/1||||||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000567014|retained_intron|||||||||||3537|-1||HGNC|HGNC:20852,G|non_coding_transcript_exon_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000575305|retained_intron|1/1||||1466|||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000647644|protein_coding|||||||||||219|-1||HGNC|HGNC:20852\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:20:26,21,0:..",
-                "chr16\t723341\tchr16_723341_G_A\tG\tA\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000219535|protein_coding|||||||||||768|1||HGNC|HGNC:14152,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000293889|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000341413|protein_coding|||||||||||3617|1||HGNC|HGNC:14177,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000345165|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389701|retained_intron|||||||||||4064|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389703|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000423653|protein_coding_CDS_not_defined|||||||||||1586|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000439619|retained_intron|||||||||||1209|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000460023|retained_intron|||||||||||1566|-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000463539|retained_intron||9/11||||||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000466708|retained_intron||10/12||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000471861|retained_intron|||||||||||1660|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000474647|retained_intron|||||||||||1782|-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000478979|retained_intron|4/4||||2296|||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000481804|retained_intron|4/5||||2627|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482152|retained_intron||3/4||||||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482878|retained_intron|4/4||||2699|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000485091|retained_intron||10/11||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000538176|retained_intron|||||||||||1201|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000544996|retained_intron|||||||||||1643|-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000549114|protein_coding|||||||||||3595|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561546|protein_coding|||||||||||3905|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561750|retained_intron|||||||||||3934|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562141|protein_coding|||||||||||3778|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562187|protein_coding|||||||||||3765|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000563792|protein_coding|||||||||||4398|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564000|protein_coding|||||||||||756|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564537|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564545|protein_coding|||||||||||3921|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564640|retained_intron|||||||||||1029|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566437|retained_intron|||||||||||833|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566525|retained_intron|||||||||||752|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567414|protein_coding|||||||||||3952|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567696|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000568141|protein_coding|||||||||||4005|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|METRN|ENSG00000103260|Transcript|ENST00000568223|protein_coding|||||||||||3686|1||HGNC|HGNC:14151,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000568916|protein_coding|||||||||||751|1|cds_start_NF|HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569143|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000569529|protein_coding|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000570237|retained_intron|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000650995|protein_coding|||||||||||2453|-1|cds_end_NF|HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000682391|retained_intron||7/9||||||||||-1||HGNC|HGNC:14153\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:19:23,21,0:..",
-                "chr16\t739761\tchr16_739761_A_G\tA\tG\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000251588|protein_coding||1/10||||||||||-1||HGNC|HGNC:14179,G|5_prime_UTR_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000540986|protein_coding|1/10||||1174|||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562421|protein_coding|||||||||||2006|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562752|retained_intron||1/4||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000563534|protein_coding_CDS_not_defined|||||||||||2297|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565065|nonsense_mediated_decay||2/5||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565341|retained_intron||1/3||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565425|nonsense_mediated_decay||1/9||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565693|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000566614|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567172|protein_coding_CDS_not_defined||1/1||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567403|protein_coding|||||||||||2009|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567455|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000568545|protein_coding|||||||||||1872|-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569604|protein_coding_CDS_not_defined|||||||||||4236|1||HGNC|HGNC:14177,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000569759|protein_coding_CDS_not_defined|||||||||||3391|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570066|nonsense_mediated_decay||1/4||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570289|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000647875|protein_coding_CDS_not_defined|||||||||||4408|1||HGNC|HGNC:14177\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:14:22,14,0:..",
-                "chr16\t766294\tchr16_766294_T_G\tT\tG\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000382862|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|upstream_gene_variant|MODIFIER|MIR662|ENSG00000207579|Transcript|ENST00000384847|miRNA|||||||||||3889|1||HGNC|HGNC:32918,G|downstream_gene_variant|MODIFIER|MSLNL|ENSG00000162006|Transcript|ENST00000543963|protein_coding|||||||||||3134|-1|cds_start_NF|HGNC|HGNC:14170,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000545450|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000561896|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563651|protein_coding||10/10||||||||||1|cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563941|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566269|protein_coding||2/7||||||||||1|cds_start_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566549|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000569566|protein_coding|||||||||||1258|1|cds_end_NF|HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER||ENSG00000279136|Transcript|ENST00000623562|TEC|||||||||||2825|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:29:29,0,43:..",
-                "chr16\t789996\tchr16_789996_T_C\tT\tC\t36\t.\tAF=0.5;AQ=36;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000007264|protein_coding|||||||||||1615|-1||HGNC|HGNC:14173,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000262315|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000317063|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000426047|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:18435,C|intron_variant&NMD_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000440239|nonsense_mediated_decay||4/13||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000455171|protein_coding||3/20||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000461268|protein_coding_CDS_not_defined|||||||||||2528|1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000464728|retained_intron||3/17||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000471202|retained_intron||4/18||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000479976|retained_intron||4/6||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000484349|retained_intron||1/3||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000491530|protein_coding_CDS_not_defined||2/5||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000493715|protein_coding_CDS_not_defined|||||||||||4706|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000561734|protein_coding|||||||||||2015|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000562070|protein_coding|||||||||||2527|-1|cds_start_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000563545|nonsense_mediated_decay|||||||||||360|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000563560|protein_coding|||||||||||1667|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565377|protein_coding|||||||||||1615|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565503|nonsense_mediated_decay|||||||||||1656|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000565787|retained_intron|||||||||||1141|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565809|protein_coding|||||||||||1625|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567114|protein_coding|||||||||||1599|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567283|nonsense_mediated_decay|||||||||||1663|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000567620|retained_intron|||||||||||703|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000569270|nonsense_mediated_decay|||||||||||255|1|cds_start_NF|HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000569601|protein_coding|||||||||||1662|-1|cds_end_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000570058|protein_coding_CDS_not_defined|||||||||||656|1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000631357|protein_coding||5/23||||||||||1||HGNC|HGNC:18435\tGT:DP:AD:GQ:PL:RNC\t0/1:15:7,8:36:36,0,49:..",
-                "chr16\t813336\tchr16_813336_T_C\tT\tC\t32\t.\tAF=0.5;AQ=32;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER||ENSG00000287855|Transcript|ENST00000655150|lncRNA|||||||||||4153|1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:14:5,9:32:32,0,39:..",
-                "chr16\t893361\tchr16_893361_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||4/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||5/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||6/7||||||||||-1||HGNC|HGNC:14154,C|upstream_gene_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000565198|retained_intron|||||||||||109|-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||3/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||4/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,45:..",
-                "chr16\t947473\tchr16_947473_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||2/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||2/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||2/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|5_prime_UTR_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding|1/6||||172|||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||2/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||2/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||2/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||2/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:23:8,15:30:29,0,47:..",
-                "chr16\t964119\tchr16_964119_A_G\tA\tG\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||1/10||||||||||-1||HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||1/7||||||||||-1||HGNC|HGNC:14154,G|missense_variant|MODERATE|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding|1/4||||4|4|2|Y/H|Tat/Cat|||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant&non_coding_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566609|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||1/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||1/9||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||1/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,G|downstream_gene_variant|MODIFIER||ENSG00000276931|Transcript|ENST00000620075|lncRNA|||||||||||4256|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:29:0,29:21:24,24,0:..",
-                "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,44:.."
-            ]
+            "ad2f3def07bee1f4bab9cfe456dada3e",
+            "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=121, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-12T10:10:59.241809478"
+        "timestamp": "2024-10-08T11:44:29.495925133"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/snv_annotation/tests/nextflow.config b/subworkflows/local/snv_annotation/tests/nextflow.config
index 2de8ad16..62fc7b69 100644
--- a/subworkflows/local/snv_annotation/tests/nextflow.config
+++ b/subworkflows/local/snv_annotation/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    withName: 'DEEPVARIANT' {
+    withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
         ext.args = { [
             '--model_type WGS',
@@ -41,7 +41,7 @@ process {
         ].join(' ')
     }
 
-    withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
+    withName: 'SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' {
         ext.prefix = { "${meta.id}_ac" }
         ext.args = [
             '--no-version',
@@ -61,7 +61,11 @@ process {
         ext.args = '-x map-hifi'
     }
 
-    withName: 'ENSEMBLVEP_VEP' {
+    withName: 'UNTAR' {
+        ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' }
+    }
+
+    withName: 'SNV_ANNOTATION:ENSEMBLVEP_SNV' {
         ext.args = { [
             '--offline',
             '--vcf',
diff --git a/subworkflows/local/structural_variant_calling.nf b/subworkflows/local/structural_variant_calling.nf
deleted file mode 100644
index be738c63..00000000
--- a/subworkflows/local/structural_variant_calling.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-include { SNIFFLES as SNIFFLES_MULTISAMPLE } from '../../modules/nf-core/sniffles/main'
-include { SNIFFLES                         } from '../../modules/nf-core/sniffles/main'
-
-workflow STRUCTURAL_VARIANT_CALLING {
-
-    take:
-    ch_bam_bai // channel: [ val(meta), [[ bam ], [bai]] ]
-    ch_fasta
-    ch_fai
-    ch_tandem_repeats
-
-    main:
-    ch_versions     = Channel.empty()
-
-    SNIFFLES (ch_bam_bai, ch_fasta, ch_tandem_repeats, true, true)
-
-    SNIFFLES.out.snf
-        .map { meta, snf -> [ [ 'id': meta.project ], snf ] }
-        .groupTuple()
-        .map { meta, snfs -> [ meta, snfs, [] ] }
-        .set{ ch_multisample_input }
-
-    SNIFFLES_MULTISAMPLE( ch_multisample_input, ch_fasta, ch_tandem_repeats, true, false )
-
-    ch_versions = ch_versions.mix(SNIFFLES.out.versions)
-    ch_versions = ch_versions.mix(SNIFFLES_MULTISAMPLE.out.versions)
-
-    emit:
-    ch_sv_calls_vcf = SNIFFLES.out.vcf             // channel: [ val(meta), vcf]
-    ch_multisample  = SNIFFLES_MULTISAMPLE.out.vcf // channel: [ val(meta), multisample.sniffles.vcf ]
-    versions        = ch_versions                  // channel: [ versions.yml ]
-}
-
diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf
index 91cb7ac5..e9c77c47 100644
--- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf
@@ -8,17 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-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 { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -35,36 +32,37 @@ include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
 // Define subworkflows and their associated "--skip"
 //
 def workflowSkips = [
-    assembly         : "skip_assembly_wf",
-    raw_read_qc      : "skip_raw_read_qc",
-    aligned_read_qc  : "skip_aligned_read_qc",
-    mapping          : "skip_mapping_wf",
-    snv_calling      : "skip_short_variant_calling",
+    assembly         : "skip_genome_assembly",
+    mapping          : "skip_alignment",
+    snv_calling      : "skip_snv_calling",
     snv_annotation   : "skip_snv_annotation",
+    sv_annotation    : "skip_sv_annotation",
     call_paralogs    : "skip_call_paralogs",
     cnv_calling      : "skip_cnv_calling",
-    phasing          : "skip_phasing_wf",
+    phasing          : "skip_phasing",
     rank_variants    : "skip_rank_variants",
     repeat_calling   : "skip_repeat_calling",
     repeat_annotation: "skip_repeat_annotation",
-    methylation      : "skip_methylation_wf",
+    methylation      : "skip_methylation_pileups",
+    qc               : "skip_qc",
 ]
 
 //
 //  E.g., the CNV-calling workflow depends on mapping and snv_calling and can't run without them.
 //
 def workflowDependencies = [
-    aligned_read_qc  : ["mapping"],
     assembly         : ["mapping"],
     call_paralogs    : ["mapping"],
     snv_calling      : ["mapping"],
+    qc               : ["mapping"],
+    sv_annotation    : ["mapping"],
     snv_annotation   : ["mapping", "snv_calling"],
     cnv_calling      : ["mapping", "snv_calling"],
     phasing          : ["mapping", "snv_calling"],
-    rank_variants    : ["mapping", "snv_calling", "snv_annotation"],
+    rank_variants    : ["mapping", "snv_calling", "snv_annotation", "sv_annotation"],
     repeat_calling   : ["mapping", "snv_calling", "phasing"],
     repeat_annotation: ["mapping", "snv_calling", "phasing", "repeat_calling"],
-    methylation      : ["mapping", "snv_calling", "phasing"],
+    methylation      : ["mapping", "snv_calling"]
 ]
 
 //
@@ -74,44 +72,47 @@ def fileDependencies = [
     mapping          : ["fasta", "somalier_sites"],
     assembly         : ["fasta", "par_regions"], // The assembly workflow should be split into two - assembly and variant calling (requires ref)
     snv_calling      : ["fasta", "par_regions"],
-    snv_annotation   : ["snp_db", "vep_cache", "vep_plugin_files", "variant_consequences_snv"],
-    cnv_calling      : ["hificnv_xy", "hificnv_xx", "hificnv_exclude"],
-    rank_variants    : ["reduced_penetrance", "score_config_snv"],
+    snv_annotation   : ["echtvar_snv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_snvs"],
+    sv_annotation    : ["svdb_sv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_svs"],
+    cnv_calling      : ["hificnv_expected_xy_cn", "hificnv_expected_xx_cn", "hificnv_excluded_regions"],
+    rank_variants    : ["genmod_reduced_penetrance", "genmod_score_config_snvs", "genmod_score_config_svs"],
     repeat_calling   : ["trgt_repeats"],
-    repeat_annotation: ["variant_catalog"],
+    repeat_annotation: ["stranger_repeat_catalog"],
 ]
 
 def parameterStatus = [
     workflow: [
-        skip_short_variant_calling: params.skip_short_variant_calling,
-        skip_phasing_wf           : params.skip_phasing_wf,
-        skip_methylation_wf       : params.skip_methylation_wf,
-        skip_rank_variants        : params.skip_rank_variants,
-        skip_repeat_calling       : params.skip_repeat_calling,
-        skip_repeat_annotation    : params.skip_repeat_annotation,
-        skip_snv_annotation       : params.skip_snv_annotation,
-        skip_call_paralogs        : params.skip_call_paralogs,
-        skip_cnv_calling          : params.skip_cnv_calling,
-        skip_mapping_wf           : params.skip_mapping_wf,
-        skip_aligned_read_qc      : params.skip_aligned_read_qc,
-        skip_raw_read_qc          : params.skip_raw_read_qc,
-        skip_assembly_wf          : params.skip_assembly_wf,
+        skip_snv_calling         : params.skip_snv_calling,
+        skip_phasing             : params.skip_phasing,
+        skip_methylation_pileups: params.skip_methylation_pileups,
+        skip_rank_variants       : params.skip_rank_variants,
+        skip_repeat_calling      : params.skip_repeat_calling,
+        skip_repeat_annotation   : params.skip_repeat_annotation,
+        skip_snv_annotation      : params.skip_snv_annotation,
+        skip_sv_annotation       : params.skip_sv_annotation,
+        skip_call_paralogs       : params.skip_call_paralogs,
+        skip_cnv_calling         : params.skip_cnv_calling,
+        skip_alignment           : params.skip_alignment,
+        skip_qc                  : params.skip_qc,
+        skip_genome_assembly     : params.skip_genome_assembly,
     ],
     files: [
-        par_regions             : params.par_regions,
-        snp_db                  : params.snp_db,
-        somalier_sites          : params.somalier_sites,
-        vep_cache               : params.vep_cache,
-        hificnv_xy              : params.hificnv_xy,
-        hificnv_xx              : params.hificnv_xx,
-        hificnv_exclude         : params.hificnv_exclude,
-        fasta                   : params.fasta,
-        trgt_repeats            : params.trgt_repeats,
-        variant_catalog         : params.variant_catalog,
-        score_config_snv        : params.score_config_snv,
-        reduced_penetrance      : params.reduced_penetrance,
-        score_config_snv        : params.score_config_snv,
-        variant_consequences_snv: params.variant_consequences_snv,
+        par_regions              : params.par_regions,
+        echtvar_snv_databases    : params.echtvar_snv_databases,
+        svdb_sv_databases        : params.svdb_sv_databases,
+        somalier_sites           : params.somalier_sites,
+        vep_cache                : params.vep_cache,
+        hificnv_expected_xy_cn   : params.hificnv_expected_xy_cn,
+        hificnv_expected_xx_cn   : params.hificnv_expected_xx_cn,
+        hificnv_excluded_regions : params.hificnv_excluded_regions,
+        fasta                    : params.fasta,
+        trgt_repeats             : params.trgt_repeats,
+        stranger_repeat_catalog  : params.stranger_repeat_catalog,
+        genmod_reduced_penetrance: params.genmod_reduced_penetrance,
+        genmod_score_config_snvs : params.genmod_score_config_snvs,
+        genmod_score_config_svs  : params.genmod_score_config_svs,
+        variant_consequences_snvs : params.variant_consequences_snvs,
+        variant_consequences_svs : params.variant_consequences_svs,
     ]
 ]
 
@@ -123,7 +124,6 @@ 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
@@ -144,47 +144,45 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
 
+
     //
     // Check config provided to the pipeline
     //
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
     validateInputParameters(parameterStatus, workflowSkips, workflowDependencies, fileDependencies)
+    validatePacBioLicense()
 
     //
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map { meta, reads ->
             [ meta.id, meta, reads ] // add sample as groupTuple key
         }
+        .groupTuple() // group by sample
         .map {
             validateInputSamplesheet(it)
         }
-        .groupTuple() // group by sample
         .map { sample, metas, reads ->
             // Add number of files per sample _after_ splitting to meta
-            [ sample, metas[0] + [n_files: metas.size() + metas.size() * Math.max(0, params.parallel_alignments - 1), single_end:true ], reads ]
+            [ sample, metas[0] + [n_files: metas.size() + metas.size() * Math.max(0, params.alignment_processes - 1), single_end:true ], reads ]
         }
         // Convert back to [ meta, reads ]
         .flatMap {
@@ -193,34 +191,21 @@ workflow PIPELINE_INITIALISATION {
         }
         .set { ch_samplesheet }
 
-        // Check that there's samples with affected phenotype if we are ranking variants
-        ch_samplesheet
-            .filter { meta, reads -> meta.phenotype == 2 }
-            .ifEmpty {
-                if(!params.skip_rank_variants) {
-                    error("No samples in samplesheet has affected phenotype (=2), --skip_rank_variants has to be active.")
-                }
-            }
+        // Check that all families has at least one sample with affected phenotype if ranking is active
+        validateAllFamiliesHasAffectedSamples(ch_samplesheet, params)
 
         // Check that there's no more than one project
-        // TODO: Try to do this in nf-schema
-        ch_samplesheet
-            .map { meta, reads -> meta.project }
-            .unique()
-            .collect()
-            .filter{ it.size() == 1 }
-            .ifEmpty {
-                error("Only one project may be specified per run")
-            }
+        validateSingleProjectPerRun(ch_samplesheet)
+
     emit:
     samplesheet = ch_samplesheet
     versions    = ch_versions
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -229,13 +214,13 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     //
@@ -243,11 +228,18 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            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)
         }
@@ -259,9 +251,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 //
 // Check and validate pipeline parameters
@@ -270,13 +262,18 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters(statusMap, workflowMap, workflowDependencies, fileDependencies) {
     genomeExistsError()
     validateParameterCombinations(statusMap, workflowMap, workflowDependencies, fileDependencies)
+
 }
 
 //
 // Validate channels from input samplesheet
 //
 def validateInputSamplesheet(input) {
-
+    // Filenames needs to be unique for each sample to avoid collisions when merging
+    fileNames = input[2].collect { new File(it.toString()).name }
+    if (fileNames.size() != fileNames.unique().size()) {
+        error "Error: Input filenames needs to be unique for each sample."
+    }
     return input
 }
 
@@ -309,167 +306,6 @@ def genomeExistsError() {
 //
 // Generate methods description for MultiQC
 //
-def toolCitationText() {
-
-    def citation_text = [
-        "MultiQC (Ewels et al. 2016)",
-        "SAMtools (Danecek et al. 2021)",
-    ]
-    if (!params.skip_raw_read_qc) {
-        citation_text = citation_text + [
-            "FastQC (Andrews 2010)",
-            "fcqrs",
-        ]
-    }
-    if (!params.skip_mapping_wf) {
-        if (params.parallel_alignments > 1) {
-            citation_text = citation_text + [
-                "splitubam",
-            ]
-        }
-        citation_text = citation_text + [
-            "SAMtools (Danecek et al. 2021)",
-            "Minimap2 (Li 2018)",
-            "Somalier (Pedersen et al. 2020)",
-            "Sniffles2 (Smolka et al. 2024)",
-        ]
-        if (!params.skip_aligned_read_qc) {
-            citation_text = citation_text + [
-                "cramino (De Coster & Rademakers 2023)",
-                "mosdepth (Pedersen & Quinlan 2018)",
-            ]
-        }
-        if (!params.skip_call_paralogs) {
-            citation_text = citation_text + [
-                "paraphase",
-            ]
-        }
-        if (!params.skip_assembly_wf) {
-            if (params.hifiasm_mode == 'trio-binning') {
-                citation_text = citation_text + [
-                    "yak",
-                ]
-            }
-            citation_text = citation_text + [
-                "Hifiasm (Cheng et al. 2021)",
-                "Gfastats (Formenti et al. 2022)",
-                "dipcall (Li et al. 2018)",
-                "SAMtools (Danecek et al. 2021)",
-                "Minimap2 (Li 2018)",
-            ]
-        }
-        if (!params.skip_short_variant_calling) {
-            citation_text = citation_text + [
-                "BEDTools (Quinlan & Hall 2010)",
-                "BCFtools (Danecek et al. 2021)",
-                "DeepVariant (Poplin et al. 2018)",
-                "GLnexus (Yun et al. 2021)",
-            ]
-        }
-        if (!params.skip_snv_annotation) {
-            citation_text = citation_text + [
-                "CADD (Rentzsch et al. 2019, Rentzsch et al. 2021)",
-                "BCFtools (Danecek et al. 2021)",
-                "VEP (McLaren et al. 2016)",
-                "Tabix (Li 2011)",
-                "Echtvar (Pedersen & de Ridder 2023)",
-            ]
-            if (!params.skip_rank_variants) {
-                citation_text = citation_text + [
-                    "Genmod (Magnusson et al. 2018)",
-                    "Tabix (Li 2011)",
-                ]
-            }
-        }
-        if (!params.skip_cnv_calling) {
-            citation_text = citation_text + [
-                "HiFiCNV",
-            ]
-        }
-        if (!params.skip_phasing_wf) {
-            citation_text = citation_text + [
-                "SAMtools (Danecek et al. 2021)",
-                "cramino (De Coster & Rademakers 2023)",
-            ]
-            if(params.phaser == 'whatshap') {
-                citation_text = citation_text + [
-                    "WhatsHap (Martin et al. 2016)",
-                ]
-            }
-            if(params.phaser == 'hiphase_sv') {
-                citation_text = citation_text + [
-                    "HiPhase (Holt et al. 2024)",
-                ]
-            }
-            if(params.phaser == 'hiphase_snv') {
-                citation_text = citation_text + [
-                    "HiPhase (Holt et al. 2024)",
-                ]
-            }
-            if (!params.skip_methylation_wf) {
-                citation_text = citation_text + [
-                    "modkit",
-                    "Tabix (Li 2011)",
-                ]
-            }
-            if (!params.skip_repeat_calling) {
-                citation_text = citation_text + [
-                    "TRGT (Dolzhenko et al. 2024)",
-                ]
-                if (!params.skip_repeat_annotation) {
-                    citation_text = citation_text + [
-                        "Stranger (Nilsson & Magnusson 2021)",
-                    ]
-                }
-            }
-        }
-    }
-
-    def return_text = "Tools used in the workflow included: " + citation_text.unique(false) { a, b -> a <=> b }.join(', ') - "" + "."
-    return return_text
-}
-
-def toolBibliographyText() {
-
-    reference_text = [
-        "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</li>",
-        "<li>Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.</li>",
-        "<li>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.</li>",
-        "<li>Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.</li>",
-        "<li>Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008</li>",
-        "<li>Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.</li>",
-        "<li>Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311</li>",
-        "<li>Rentzsch P, Schubach M, Shendure J, Kircher M. CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 2021;13(1):31. doi:10.1186/s13073-021-00835-9</li>",
-        "<li>Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. 2019;47(D1):D886-D894. doi:10.1093/nar/gky1016</li>",
-        "<li>Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235</li>",
-        "<li>Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D (2018) A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods, 15:595-597. [PMID:30013044]</li>",
-        "<li>Brent S Pedersen, Jeroen de Ridder, Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels, Nucleic Acids Research, Volume 51, Issue 1, 11 January 2023, Page e3, https://doi.org/10.1093/nar/gkac931</li>",
-        "<li>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</li>",
-        "<li>Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].</li>",
-        "<li>Magnusson M, Hughes T, Glabilloy, Bitdeli Chef. genmod: Version 3.7.3. Published online November 15, 2018. doi:10.5281/ZENODO.3841142</li>",
-        "<li>Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, https://doi.org/10.1093/bioinformatics/btac460</li>",
-        "<li>Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081</li>",
-        "<li>Cheng, H., Concepcion, G.T., Feng, X. et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5</li>",
-        "<li>James M Holt, Christopher T Saunders, William J Rowell, Zev Kronenberg, Aaron M Wenger, Michael Eberle, HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing, Bioinformatics, Volume 40, Issue 2, February 2024, btae042, https://doi.org/10.1093/bioinformatics/btae042</li>",
-        "<li>Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191</li>",
-        "<li>Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699</li>",
-        "<li>Genome-wide profiling of highly similar paralogous genes using HiFi sequencing. Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M Devaney, Jessica Noya, April S Berlyoung, Rhonda Brandon, Kathleen S Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, UCI Genomics Research to Elucidate the Genetics of Rare Diseases (UCI GREGoR) Consortium, Michael A Eberle. bioRxiv 2024.04.19.590294; doi: https://doi.org/10.1101/2024.04.19.590294</li>",
-        "<li>Smolka, M., Paulin, L.F., Grochowski, C.M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02024-y</li>",
-        "<li>Pedersen, B.S., Bhetariya, P.J., Brown, J. et al. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Med 12, 62 (2020). https://doi.org/10.1186/s13073-020-00761-2</li>",
-        "<li>Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873</li>",
-        "<li>Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011;27(5):718-719. doi:10.1093/bioinformatics/btq671</li>",
-        "<li>Dolzhenko, E., English, A., Dashnow, H. et al. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02057-3</li>",
-        "<li>Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O Fischer, Nadia Pisanti, Gunnar W Klau, Alexander Schöenhuth, Tobias Marschall. bioRxiv 085050; doi: https://doi.org/10.1101/085050</li>",
-        "<li>Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.</li>",
-        "<li>Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.</li>",
-        "<li>da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.</li>",
-        "<li>Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.</li>",
-        "<li>Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.</li>",
-    ].join(' ').trim()
-
-    return reference_text
-}
-
 def methodsDescriptionText(mqc_methods_yaml) {
     // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
@@ -482,19 +318,14 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     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"] = ""
-
-    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    meta["tool_bibliography"] = toolBibliographyText()
-
     def methods_text = mqc_methods_yaml.text
 
     def engine =  new groovy.text.SimpleTemplateEngine()
@@ -503,6 +334,52 @@ def methodsDescriptionText(mqc_methods_yaml) {
     return description_html.toString()
 }
 
+def extractSoftwareFromVersions(module_yaml_file) {
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def yamlData = yaml.load(module_yaml_file)
+    // Extract all software (keys) from a module yaml
+    def softwareInModule = yamlData.values().collect { it.keySet() }.flatten()
+    return softwareInModule
+}
+
+def generateReferenceHTML(tool_list, description) {
+    def items = tool_list
+        .collect { it.trim() }
+        .unique()              // samtools and bcftools share reference
+        .findAll { it != "" }  // some tools does not have a reference, e.g. awk, gunzip
+
+    if (description == 'citation') {
+        return "  <p>Tools used in the workflow included: ${items.join(', ')}.</p>"
+    } else if (description == 'bibliography') {
+        return "  <h4>References</h4><ul><li>${items.join('</li><li>')}</li></ul>"
+    }
+}
+
+def citationBibliographyText(ch_versions, references_yaml, description) {
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def softwareReferences = yaml.load(references_yaml.text).tool
+
+    def unwantedReferences = ['genomic-medicine-sweden/nallo', 'Nextflow']
+    // These are not collected in ch_versions but should be referenced
+    baseTools = Channel.from(['nextflow', 'nf_core', 'bioconda', 'biocontainers', 'multiqc'])
+
+    ch_versions
+        .map { module_yaml -> extractSoftwareFromVersions(module_yaml) }
+        .flatten() // split multi-tool modules
+        .unique()
+        .filter { tool -> !unwantedReferences.contains(tool) }
+        .concat(baseTools)
+        .collect { tool ->
+            def toolDetails = softwareReferences[tool]
+            if (toolDetails == null) {
+                throw new IllegalStateException("Tool: '${tool}' not found in ${references_yaml}")
+            }
+            return toolDetails[description]
+        }
+        .sort()
+        .map { tools -> generateReferenceHTML(tools, description) }
+}
+
 //
 // Validate  workflow skip combinations
 //
@@ -626,3 +503,56 @@ def findKeyForValue(def valueToFind, Map map) {
     return null // Value not found
 }
 
+// Utility function to create channels from references
+def createReferenceChannelFromPath(param, defaultValue = '') {
+    return param ? Channel.fromPath(param, checkIfExists: true)
+        .map { [ [ id: it.simpleName ], it ] }
+        .collect() : defaultValue
+}
+// Utility function to create channels from samplesheets
+def createReferenceChannelFromSamplesheet(param, schema, defaultValue = '') {
+    return param ? Channel.fromList(samplesheetToList(param, schema)) : defaultValue
+}
+
+def validatePacBioLicense() {
+    if (params.phaser.matches('hiphase') && params.preset == 'ONT_R10') {
+        error "ERROR: The HiPhase license only permits analysis of data from PacBio."
+    }
+}
+
+// Genmod within RANK_VARIANTS requires affected individuals in the samplesheet.
+// This is a convenience function to fail early if there are families without affected individuals.
+def validateAllFamiliesHasAffectedSamples(ch_samplesheet, params) {
+
+    if (params.skip_rank_variants) {
+        return
+    }
+
+    def familiesWithPhenotypes = ch_samplesheet
+        .map { meta, reads -> [ meta.family_id, meta.phenotype ] }
+        .groupTuple()
+
+    def familiesWithoutAffected = familiesWithPhenotypes
+        .filter { family, phenotype -> !phenotype.contains(2) }
+
+    familiesWithoutAffected
+        .map { family, phenotype -> family }
+        .collect()
+        .subscribe { familyList ->
+            if (familyList) {
+                error("ERROR: No samples in families: ${familyList.join(", ")} have affected phenotype (=2); --skip_rank_variants has to be active.")
+            }
+        }
+}
+
+def validateSingleProjectPerRun(ch_samplesheet) {
+    def oneProject = ch_samplesheet
+        .map { meta, reads -> meta.project }
+        .unique()
+        .collect()
+        .filter{ it.size() == 1 }
+
+    if(!oneProject) {
+        error("Only one project may be specified per run")
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f..0fcbf7b3 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,18 +2,13 @@
 // 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
@@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -76,13 +71,13 @@ def getWorkflowVersion() {
 // 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)
+    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   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,37 +85,40 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.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
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // 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 required_channels_in_order = ['conda-forge', 'bioconda']
     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]))
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf..a09572e5 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    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/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c39..5cb7bafe 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,17 +2,13 @@
 // 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
 
@@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${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
@@ -52,12 +45,14 @@ def checkConfigProvided() {
 //
 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"
+        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 `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${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"
+        )
     }
 }
 
@@ -66,25 +61,21 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Handling multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +93,8 @@ def getWorkflowVersion() {
 // 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 ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -113,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -122,11 +113,7 @@ def workflowVersionToYAML() {
 // 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()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -134,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 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>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        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"
             }
-            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}"
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${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
 }
@@ -161,7 +154,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +173,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +181,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -200,54 +193,54 @@ def logColours(monochrome_logs=true) {
     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"
+    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"
+    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"
+    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"
+    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"
+    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
 }
@@ -262,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -281,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 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: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            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
+    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 = [:]
@@ -338,39 +341,41 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // 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: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${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)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${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(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${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(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
     output_tf.delete()
 }
 
@@ -378,15 +383,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     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) ${colors.reset}-"
+            log.info("-${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${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -395,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            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
+    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()
@@ -434,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    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());
+    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_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 00000000..4994303e
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 00000000..f7d9f028
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 00000000..8fb30164
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 00000000..0907ac58
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c9..331e0d2f 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65d..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// 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
deleted file mode 100644
index 3d4a6b04..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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
deleted file mode 100644
index 5784a33f..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-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/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..3ed901fb
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,24 @@
+aligned_reads/**/*.{bam,bai}
+cnv_calling/**/*.log
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/multiqc_somalier.txt
+multiqc/multiqc_data/somalier_*_plot.txt
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt
+multiqc/multiqc_plots/**/*.{pdf,svg,txt,png}
+multiqc/multiqc_report.html
+paraphase/**/*.{vcf.gz,tbi,bam,bai,json}
+phased_variants/**/*.{vcf.gz,tbi}
+pipeline_info/*.{html,json,txt,yml}
+qc/cramino/**/*.txt
+qc/fastqc/**/*.{zip,html}
+qc/somalier/**/*.{html,tsv}
+qc/deepvariant_vcfstatsreport/**/*.html
+repeats/**/*.{vcf.gz,tbi,bam,bai}
+snvs/**/*.{vcf.gz,tbi,txt}
+svs/**/*.{vcf.gz,tbi}
diff --git a/tests/.nftignore_unstable_variants b/tests/.nftignore_unstable_variants
new file mode 100644
index 00000000..56a5b475
--- /dev/null
+++ b/tests/.nftignore_unstable_variants
@@ -0,0 +1,4 @@
+paraphase/**/*.vcf.gz
+phased_variants/**/*.vcf.gz
+snvs/**/*.vcf.gz
+svs/**/*.vcf.gz
diff --git a/tests/main.nf.test b/tests/main.nf.test
deleted file mode 100644
index 7a79b71f..00000000
--- a/tests/main.nf.test
+++ /dev/null
@@ -1,345 +0,0 @@
-nextflow_pipeline {
-
-    name "Test pipeline GENOMICMEDICINESWEDEN_NALLO"
-    script "../main.nf"
-    profile "test"
-    tag "PIPELINE"
-
-    test("test profile") {
-        tag "samplesheet"
-
-        when {
-            params {
-                // Base directory for genomic-medicine-sweden/nallo test data
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/'
-                // Test files
-                fasta                    = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
-                input                    = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
-                bed                      = params.pipelines_testdata_base_path + 'reference/test_data.bed'
-                hificnv_xy               = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
-                hificnv_xx               = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
-                hificnv_exclude          = params.pipelines_testdata_base_path + 'reference/empty.bed'
-                par_regions              = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
-                trgt_repeats             = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
-                variant_catalog          = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
-                vep_cache                = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
-                vep_plugin_files         = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
-                snp_db                   = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
-                somalier_sites           = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
-                reduced_penetrance       = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
-                score_config_snv         = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
-                variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
-
-                // Parameters
-                parallel_snv    = 2
-                preset          = "revio"
-                outdir          = "$outputDir"
-            }
-        }
-
-        then {
-            assertAll (
-                { assert workflow.success },
-                // Assert with snapshot multisample
-                { assert snapshot(
-                    file("$outputDir/pedigree/test.ped"),
-                    file("$outputDir/qc_aligned_reads/somalier/relate/test/test.pairs.tsv"),
-                    file("$outputDir/qc_aligned_reads/somalier/relate/test/test.samples.tsv"),
-                    file("$outputDir/qc_aligned_reads/somalier/relate/test/test.html"),
-                    file("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    file("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    file("$outputDir/multiqc/multiqc_data/multiqc_somalier.txt"),
-                    // Assert with snapshot HG002_Revio
-                    bam("$outputDir/aligned_reads/HG002_Revio/HG002_Revio_phased.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary"),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam", stringency: 'silent').getReadsMD5(),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bed"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.copynum.bedgraph"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.depth.bw"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.maf.bw"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.global.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.region.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.mosdepth.summary.txt"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.vcf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.pair.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.HG002_Revio.vcf.gz.tbi"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio/HG002_Revio_modkit_pileup.bed.gz"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio/HG002_Revio_modkit_pileup.bed.gz.tbi"),
-                    bam("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.arrow"),
-                    file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.arrow"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz.csi"),
-                    file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio/HG002_PacBio_Revio.fastq.gz.tsv.zst"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_sorted.vcf.gz"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_sorted.vcf.gz.tbi"),
-                    bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/snvs/stats/single_sample/HG002_Revio.vcf.gz.bcftools_stats.txt").readLines()[0..2],
-                ).match() },
-                // Assert exists multisample
-                { assert new File("$outputDir/databases/echtvar/encode/test/test.zip").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_data.json").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc.log").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() },
-                { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz.tbi").exists() },
-                // Assert exists HG002_Revio
-                { assert new File("$outputDir/aligned_reads/HG002_Revio/HG002_Revio_phased.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.sam.gz").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.sam.gz").exists() },
-                { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio/HG002_Revio.log").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_1.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_1.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_2.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_2.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_ungrouped.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio/HG002_Revio_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.bam.bai").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio/HG002_Revio.paraphase.json").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.txt").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.txt").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio/HG002_Revio_phased.vcf.gz").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio/HG002_Revio_phased.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio/HG002_Revio_stats.stats.tsv").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio/HG002_Revio_stats.blocks.tsv").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio/HG002_Revio_fastqc.html").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio/HG002_Revio_fastqc.zip").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam.bai").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.snf").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz.tbi").exists() }
-            )
-        }
-    }
-
-    test("test profile - multisample") {
-        tag "samplesheet_multisample_bam"
-
-        when {
-            params {
-                // Base directory for genomic-medicine-sweden/nallo test data
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/'
-                // Test files
-                fasta                    = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
-                input                    = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam.csv'
-                bed                      = params.pipelines_testdata_base_path + 'reference/test_data.bed'
-                hificnv_xy               = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed'
-                hificnv_xx               = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed'
-                hificnv_exclude          = params.pipelines_testdata_base_path + 'reference/empty.bed'
-                par_regions              = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed'
-                trgt_repeats             = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed'
-                variant_catalog          = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json'
-                vep_cache                = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz'
-                vep_plugin_files         = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv'
-                snp_db                   = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv'
-                somalier_sites           = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
-                reduced_penetrance       = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
-                score_config_snv         = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
-                variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
-
-                // Parameters
-                parallel_snv    = 2
-                preset          = "revio"
-                outdir          = "$outputDir"
-            }
-        }
-
-        then {
-            assertAll (
-                { assert workflow.success },
-                // Assert with snapshot multisample
-                { assert snapshot(
-                    file("$outputDir/pedigree/test.ped"),
-                    file("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    file("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    // Assert with snapshot HG002_Revio_A
-                    bam("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.assembly_summary"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.assembly_summary"),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam", stringency: 'silent').getReadsMD5(),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bed"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.copynum.bedgraph"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.depth.bw"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.maf.bw"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.global.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.region.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.mosdepth.summary.txt"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.vcf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.pair.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.HG002_Revio_A.vcf.gz.tbi"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_A/HG002_Revio_A_modkit_pileup.bed.gz"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_A/HG002_Revio_A_modkit_pileup.bed.gz.tbi"),
-                    bam("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_A/HG002_Revio_A_cramino_aligned_phased.arrow"),
-                    file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_A/HG002_Revio_A_cramino_aligned.arrow"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.regions.bed.gz"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_A/HG002_Revio_A.regions.bed.gz.csi"),
-                    file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio_A/HG002_PacBio_Revio.bam_other.fastq.gz.tsv.zst"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz.tbi"),
-                    bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/snvs/stats/single_sample/HG002_Revio_A.vcf.gz.bcftools_stats.txt").readLines()[0..2],
-                    // Assert with snapshot HG002_Revio_B
-                    bam("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.assembly_summary"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.assembly_summary"),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam", stringency: 'silent').getReadsMD5(),
-                    bam("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bed"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bed"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.copynum.bedgraph"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.depth.bw"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.maf.bw"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.global.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.region.dist.txt"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.mosdepth.summary.txt"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.fasta.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.vcf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.paf.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.var.gz"),
-                    file("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.pair.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.vcf.gz"),
-                    file("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.HG002_Revio_B.vcf.gz.tbi"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_B/HG002_Revio_B_modkit_pileup.bed.gz"),
-                    file("$outputDir/methylation/modkit/pileup/unphased/HG002_Revio_B/HG002_Revio_B_modkit_pileup.bed.gz.tbi"),
-                    bam("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_B/HG002_Revio_B_cramino_aligned_phased.arrow"),
-                    file("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_B/HG002_Revio_B_cramino_aligned.arrow"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.regions.bed.gz"),
-                    file("$outputDir/qc_aligned_reads/mosdepth/HG002_Revio_B/HG002_Revio_B.regions.bed.gz.csi"),
-                    file("$outputDir/qc_raw_reads/fqcrs/HG002_Revio_B/HG002_Revio_B.merged.fastq.gz.tsv.zst"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz"),
-                    file("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz.tbi"),
-                    bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam", stringency: 'silent').getReadsMD5(),
-                    file("$outputDir/snvs/stats/single_sample/HG002_Revio_B.vcf.gz.bcftools_stats.txt").readLines()[0..2],
-                ).match() },
-                // Assert exists multisample - note the trgt multisample that doesn't exist in singlesample
-                { assert new File("$outputDir/databases/echtvar/encode/test/test.zip").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.pairs.tsv").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.samples.tsv").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/somalier/relate/test/test.html").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_somalier.txt").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_data.json").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc.log").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() },
-                { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() },
-                { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/multi_sample/test/test_sniffles.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() },
-                // Assert exists HG002_Revio_A
-                { assert new File("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.sam.gz").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.sam.gz").exists() },
-                { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio_A/HG002_Revio_A.log").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_1.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_1.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_2.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_2.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_ungrouped.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_A/HG002_Revio_A_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.bam.bai").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A_paraphase_vcfs/HG002_Revio_A_hba.vcf.gz").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A_paraphase_vcfs/HG002_Revio_A_hba.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_A/HG002_Revio_A.paraphase.json").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_A/HG002_Revio_A_cramino_aligned_phased.txt").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_A/HG002_Revio_A_cramino_aligned.txt").exists() },
-                { assert new File("$outputDir/aligned_reads/HG002_Revio_A/HG002_Revio_A_phased.bam.bai").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_A/HG002_Revio_A_phased.vcf.gz").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_A/HG002_Revio_A_phased.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_A/HG002_Revio_A_stats.stats.tsv").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_A/HG002_Revio_A_stats.blocks.tsv").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_A/HG002_Revio_A_fastqc.html").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_A/HG002_Revio_A_fastqc.zip").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam.bai").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.snf").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz.tbi").exists() },
-                // Assert exists HG002_Revio_B
-                { assert new File("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.sam.gz").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam.bai").exists() },
-                { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.sam.gz").exists() },
-                { assert new File("$outputDir/cnv_calling/hificnv/HG002_Revio_B/HG002_Revio_B.log").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_1.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_1.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_2.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_2.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_ungrouped.bed.gz").exists() },
-                { assert new File("$outputDir/methylation/modkit/pileup/phased/HG002_Revio_B/HG002_Revio_B_modkit_pileup_phased_ungrouped.bed.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.bam.bai").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B_paraphase_vcfs/HG002_Revio_B_hba.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/paraphase/HG002_Revio_B/HG002_Revio_B.paraphase.json").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/phased/HG002_Revio_B/HG002_Revio_B_cramino_aligned_phased.txt").exists() },
-                { assert new File("$outputDir/qc_aligned_reads/cramino/unphased/HG002_Revio_B/HG002_Revio_B_cramino_aligned.txt").exists() },
-                { assert new File("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_phased.bam.bai").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_B/HG002_Revio_B_phased.vcf.gz").exists() },
-                { assert new File("$outputDir/phasing/whatshap/phase/HG002_Revio_B/HG002_Revio_B_phased.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_B/HG002_Revio_B_stats.stats.tsv").exists() },
-                { assert new File("$outputDir/phasing/whatshap/stats/HG002_Revio_B/HG002_Revio_B_stats.blocks.tsv").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_B/HG002_Revio_B_fastqc.html").exists() },
-                { assert new File("$outputDir/qc_raw_reads/fastqc/HG002_Revio_B/HG002_Revio_B_fastqc.zip").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz").exists() },
-                { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam.bai").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz").exists() },
-                { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz.tbi").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.snf").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz").exists() },
-                { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz.tbi").exists() }
-            )
-        }
-    }
-}
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
deleted file mode 100644
index a3412aba..00000000
--- a/tests/main.nf.test.snap
+++ /dev/null
@@ -1,150 +0,0 @@
-{
-    "test profile": {
-        "content": [
-            "test.ped:md5,bd5cec27ba7337a85cf98e787131e2b5",
-            "test.pairs.tsv:md5,4a0988fc3c0fe5cfd5dd205fe6755595",
-            "test.samples.tsv:md5,1685dc6cb8c6b9806ca636662980d686",
-            "test.html:md5,d05e0eceb70ada3a0c25f99a16ad1889",
-            "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
-            "multiqc_fastqc.txt:md5,c60b523b5f11c07c9149043bf68f92ad",
-            "multiqc_somalier.txt:md5,20b4c5b2d5b94b77fb800548e07a874e",
-            "74b4822241bd8d1bc42f494f1f3e326c",
-            "HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary:md5,ccaad2690abccadc4ec3b2c5d8fa4b05",
-            "HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary:md5,c5bbeabb571453186a39cf6e487dbcc5",
-            "67fc08c5db63d417992aa4842a567c2d",
-            "28f964b0683d285fabc5407af0f28580",
-            "HG002_Revio.dip.bed:md5,5c0ad25a4bb82b8ce06f526664ffbd1c",
-            "HG002_Revio.hap1.bed:md5,28ac0570c41a83c231f2c853918d24c5",
-            "HG002_Revio.hap2.bed:md5,8b9a998402277ef043718f95a5410fe1",
-            "HG002_Revio.HG002_Revio.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
-            "HG002_Revio.HG002_Revio.depth.bw:md5,20757c985f4713b8568dee05765db701",
-            "HG002_Revio.HG002_Revio.maf.bw:md5,4699d7a664277863f06eb48c3cba3c41",
-            "HG002_Revio.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
-            "HG002_Revio.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
-            "HG002_Revio.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
-            "HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz:md5,6c040d554c3310e1555c928a68fca9f2",
-            "HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz:md5,d250ea1f1a1186d1d324c843bc8a3e7a",
-            "HG002_Revio.dip.vcf.gz:md5,ce28d131a954db1325246fce498eb659",
-            "HG002_Revio.hap1.paf.gz:md5,493bbf9db4bc541a348de656f29e58f1",
-            "HG002_Revio.hap1.var.gz:md5,55e7be8fb8fe051725890f1cfaae3692",
-            "HG002_Revio.hap2.paf.gz:md5,63066bc6d6abcdff9b6916d549077a41",
-            "HG002_Revio.hap2.var.gz:md5,fb0b9d9708cd907831f9cd7019f1d03d",
-            "HG002_Revio.pair.vcf.gz:md5,977d60dfdf18e27c06574ec8297e49e4",
-            "HG002_Revio.HG002_Revio.vcf.gz:md5,771f7d9ecbd161dedfbdd053ceff0d52",
-            "HG002_Revio.HG002_Revio.vcf.gz.tbi:md5,65d6930f79e626a5542091b7a419dc2b",
-            "HG002_Revio_modkit_pileup.bed.gz:md5,8850d8414ecefc2341452f23ce5e6870",
-            "HG002_Revio_modkit_pileup.bed.gz.tbi:md5,af7e0b1699351d6df3d93d223d5c3da9",
-            "fcc3f220bb09d3264f97e7f620779be0",
-            "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
-            "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
-            "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
-            "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
-            "HG002_PacBio_Revio.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b",
-            "HG002_Revio_sorted.vcf.gz:md5,fbb5699b8f74fc105fb154e8fac7bfea",
-            "HG002_Revio_sorted.vcf.gz.tbi:md5,0466518ee265ba63160ed27cee0dec88",
-            "65999ab8f2bc7841de8172468bf23ab6",
-            [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
-                "# The command line was:\tbcftools stats  HG002_Revio.vcf.gz",
-                "#"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-08-29T10:42:09.011660883"
-    },
-    "test profile - multisample": {
-        "content": [
-            "test.ped:md5,db74c6787a92a70ffaab766fa4d7a873",
-            "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
-            "multiqc_fastqc.txt:md5,b74145ef9fbf8addcc2997ca26b3aa45",
-            "74b4822241bd8d1bc42f494f1f3e326c",
-            "HG002_Revio_A.asm.bp.hap1.p_ctg.assembly_summary:md5,ccaad2690abccadc4ec3b2c5d8fa4b05",
-            "HG002_Revio_A.asm.bp.hap2.p_ctg.assembly_summary:md5,c5bbeabb571453186a39cf6e487dbcc5",
-            "67fc08c5db63d417992aa4842a567c2d",
-            "28f964b0683d285fabc5407af0f28580",
-            "HG002_Revio_A.dip.bed:md5,5c0ad25a4bb82b8ce06f526664ffbd1c",
-            "HG002_Revio_A.hap1.bed:md5,28ac0570c41a83c231f2c853918d24c5",
-            "HG002_Revio_A.hap2.bed:md5,8b9a998402277ef043718f95a5410fe1",
-            "HG002_Revio_A.HG002_Revio_A.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
-            "HG002_Revio_A.HG002_Revio_A.depth.bw:md5,20757c985f4713b8568dee05765db701",
-            "HG002_Revio_A.HG002_Revio_A.maf.bw:md5,4699d7a664277863f06eb48c3cba3c41",
-            "HG002_Revio_A.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
-            "HG002_Revio_A.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
-            "HG002_Revio_A.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
-            "HG002_Revio_A.asm.bp.hap1.p_ctg.fasta.gz:md5,6c040d554c3310e1555c928a68fca9f2",
-            "HG002_Revio_A.asm.bp.hap2.p_ctg.fasta.gz:md5,d250ea1f1a1186d1d324c843bc8a3e7a",
-            "HG002_Revio_A.dip.vcf.gz:md5,d97b3e520a3bf6f85eb6b5dd66961e71",
-            "HG002_Revio_A.hap1.paf.gz:md5,493bbf9db4bc541a348de656f29e58f1",
-            "HG002_Revio_A.hap1.var.gz:md5,55e7be8fb8fe051725890f1cfaae3692",
-            "HG002_Revio_A.hap2.paf.gz:md5,63066bc6d6abcdff9b6916d549077a41",
-            "HG002_Revio_A.hap2.var.gz:md5,fb0b9d9708cd907831f9cd7019f1d03d",
-            "HG002_Revio_A.pair.vcf.gz:md5,8fd0eb40954ed6d829d0632d0cf54414",
-            "HG002_Revio_A.HG002_Revio_A.vcf.gz:md5,e575fbadcd826243561192310f234c82",
-            "HG002_Revio_A.HG002_Revio_A.vcf.gz.tbi:md5,e27fe63e51a2cfaec020ad0a1aec4a7f",
-            "HG002_Revio_A_modkit_pileup.bed.gz:md5,8850d8414ecefc2341452f23ce5e6870",
-            "HG002_Revio_A_modkit_pileup.bed.gz.tbi:md5,af7e0b1699351d6df3d93d223d5c3da9",
-            "fcc3f220bb09d3264f97e7f620779be0",
-            "HG002_Revio_A_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
-            "HG002_Revio_A_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
-            "HG002_Revio_A.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
-            "HG002_Revio_A.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
-            "HG002_PacBio_Revio.bam_other.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b",
-            "HG002_Revio_A_sorted.vcf.gz:md5,680938d6ebeafe73d8df0b21c0310276",
-            "HG002_Revio_A_sorted.vcf.gz.tbi:md5,a6554ab817e7c232a1554ea85fa00151",
-            "65999ab8f2bc7841de8172468bf23ab6",
-            [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
-                "# The command line was:\tbcftools stats  HG002_Revio_A.vcf.gz",
-                "#"
-            ],
-            "fe7bb70701d1100b2874c10a512a2144",
-            "HG002_Revio_B.asm.bp.hap1.p_ctg.assembly_summary:md5,4941730ceacb4012e771208be7a6673a",
-            "HG002_Revio_B.asm.bp.hap2.p_ctg.assembly_summary:md5,be7dcb093d25922b72ef0f7bc1bf0706",
-            "dc5ae77e003989e86ccbfd14b4ae6c7",
-            "3608f178b942e804e5588e5bbd9e06ee",
-            "HG002_Revio_B.dip.bed:md5,865dbd07d7c6b7904176ee25cce91928",
-            "HG002_Revio_B.hap1.bed:md5,50609668f7b26a9d68d583fdaad9bedd",
-            "HG002_Revio_B.hap2.bed:md5,865338ef4e621ca1e8efcc0a8a6c64d0",
-            "HG002_Revio_B.HG002_Revio_B.copynum.bedgraph:md5,22b040fce6bdf6b2e323f1cc1658128d",
-            "HG002_Revio_B.HG002_Revio_B.depth.bw:md5,26bc36669ae0b066c2462e3c9307860f",
-            "HG002_Revio_B.HG002_Revio_B.maf.bw:md5,6c5691dbaf6e526f4b8fa0f7147bfc8b",
-            "HG002_Revio_B.mosdepth.global.dist.txt:md5,c3449580a34c495f537635c3bde4699d",
-            "HG002_Revio_B.mosdepth.region.dist.txt:md5,98a20c6295a956932c21534cbf5e889c",
-            "HG002_Revio_B.mosdepth.summary.txt:md5,d4fa8aeabc3b348255e7a2fa0135b1a4",
-            "HG002_Revio_B.asm.bp.hap1.p_ctg.fasta.gz:md5,bd4ae3d478b26ebaa6b64c6795e09e71",
-            "HG002_Revio_B.asm.bp.hap2.p_ctg.fasta.gz:md5,688d9e693b580a901632022b26fd9d5f",
-            "HG002_Revio_B.dip.vcf.gz:md5,544c42489591d02fa0dc143e6cf1c6b8",
-            "HG002_Revio_B.hap1.paf.gz:md5,467daced5b3897cf74c68251b8f99e3a",
-            "HG002_Revio_B.hap1.var.gz:md5,fb4efe049800a27b10d080ea5a563fb6",
-            "HG002_Revio_B.hap2.paf.gz:md5,fadac5cffae4e167ef1c41de929edf1b",
-            "HG002_Revio_B.hap2.var.gz:md5,6e4fcd586c9a30b46d23a8de1d0efe73",
-            "HG002_Revio_B.pair.vcf.gz:md5,987d192995729f82247dffdcea2dd60f",
-            "HG002_Revio_B.HG002_Revio_B.vcf.gz:md5,59773d5836f76b36dc1bf75e32186898",
-            "HG002_Revio_B.HG002_Revio_B.vcf.gz.tbi:md5,1408aeaca23a00eee979101eb45d887d",
-            "HG002_Revio_B_modkit_pileup.bed.gz:md5,e50e61d644ad3219b3088b1c0d701862",
-            "HG002_Revio_B_modkit_pileup.bed.gz.tbi:md5,ae29296657f0d2c7451d285ec49f8675",
-            "a8a1403ba192f971638c870a2be35700",
-            "HG002_Revio_B_cramino_aligned_phased.arrow:md5,bdd385c0b007ffc30c6cfdd98b15ed82",
-            "HG002_Revio_B_cramino_aligned.arrow:md5,bdd385c0b007ffc30c6cfdd98b15ed82",
-            "HG002_Revio_B.regions.bed.gz:md5,deaca22783bd058cdc8756efa25b5f53",
-            "HG002_Revio_B.regions.bed.gz.csi:md5,dd9a0d36d71da0d274d1c9ca6f8571ae",
-            "HG002_Revio_B.merged.fastq.gz.tsv.zst:md5,0641e175a07429b61710329a2eeef450",
-            "HG002_Revio_B_sorted.vcf.gz:md5,ce617741468f4bc7f504f8f488332098",
-            "HG002_Revio_B_sorted.vcf.gz.tbi:md5,e255a5ea92885967f0c126bddc8ea3b2",
-            "6b0cf3f492ce898398835d1102afd369",
-            [
-                "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
-                "# The command line was:\tbcftools stats  HG002_Revio_B.vcf.gz",
-                "#"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-08-29T10:45:44.41793623"
-    }
-}
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index 2aa3910c..00000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1,77 +0,0 @@
-params {
-    // Base directory for nf-core/modules test data
-    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-
-    // Base directory for genomic-medicine-sweden/nallo test data
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/'
-
-    max_cpus   = 4
-    max_memory = '15.GB'
-    max_time   = '6.h'
-
-}
-
-// Impose same minimum Nextflow version as the pipeline for testing
-manifest {
-    nextflowVersion = '!>=23.04.0'
-}
-
-// Disable all Nextflow reporting options
-timeline { enabled = false }
-report   { enabled = false }
-trace    { enabled = false }
-dag      { enabled = false }
-
-process {
-
-    withLabel: 'process_high' {
-        cpus = 4
-    }
-
-    withLabel: 'process_medium' {
-        cpus = 2
-    }
-
-    withLabel: 'process_low' {
-        cpus = 1
-    }
-
-    withLabel: 'process_single' {
-        cpus = 1
-    }
-
-    withName: '.*:NALLO:ASSEMBLY:HIFIASM' {
-
-        ext.args = '-f0'
-    }
-
-    withName: '.*:CALL_PARALOGS:PARAPHASE' {
-
-        ext.args = '--gene hba'
-    }
-
-    withName: '.*:NALLO:PHASING:WHATSHAP_PHASE' {
-
-        ext.args = '--ignore-read-groups --indels --distrust-genotypes --include-homozygous'
-    }
-
-    withName: '.*:NALLO:SNV_ANNOTATION:ENSEMBLVEP_VEP' {
-        ext.prefix = { "${meta.id}_vep" }
-        ext.args = { [
-            "--dir_plugins .",
-            "--plugin LoFtool,LoFtool_scores.txt",
-            "--plugin pLI,pLI_values.txt",
-            "--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz",
-            '--distance 5000',
-            '--buffer_size 20000',
-            '--format vcf --max_sv_size 248387328',
-            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
-            '--domains --exclude_predicted --force_overwrite',
-            '--hgvs --humdiv --no_progress --numbers',
-            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
-            '--uniprot --vcf',
-            '--no_stats'
-        ].join(' ') }
-    }
-
-}
diff --git a/tests/samplesheet.nf.test b/tests/samplesheet.nf.test
new file mode 100644
index 00000000..ea02a959
--- /dev/null
+++ b/tests/samplesheet.nf.test
@@ -0,0 +1,51 @@
+nextflow_pipeline {
+
+    name "Test pipeline GENOMICMEDICINESWEDEN_NALLO"
+    script "../main.nf"
+    tag "PIPELINE"
+
+    test("test profile") {
+        tag "samplesheet"
+
+        when {
+            params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
+                input                        = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv'
+                outdir                       = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name      = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path      = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files        = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            // all_vcf_files: All vcf files - can have unstable variants and/or unstable headers
+            def all_vcf_files    = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
+            // stable_vcf_files: Vcf files with stable variants - can be snapshot unsing variantsMD5
+            def stable_vcf_files = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore_unstable_variants', include: ['**/*.vcf.gz'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nallo_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString(), stringency: 'silent').getReadsMD5() ] },
+                    // All vcf files
+                    all_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.summary ] },
+                    // Stable vcf files
+                    stable_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5 ] }
+                ).match() }
+            )
+        }
+    }
+
+}
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
new file mode 100644
index 00000000..7036b956
--- /dev/null
+++ b/tests/samplesheet.nf.test.snap
@@ -0,0 +1,678 @@
+{
+    "test profile": {
+        "content": [
+            116,
+            {
+                "ADD_FOUND_IN_TAG": {
+                    "bcftools": 1.2,
+                    "busybox_awk": "1.36.1"
+                },
+                "ADD_MOST_SEVERE_CSQ": {
+                    "add_most_severe_consequence": 1.0,
+                    "python": "3.8.3"
+                },
+                "ADD_MOST_SEVERE_PLI": {
+                    "add_most_severe_pli": 1.0,
+                    "python": "3.8.3"
+                },
+                "BCFTOOLS_CONCAT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS_ANNO": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_INDEX": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_MULTISAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_SINGLESAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_PLUGINSPLIT_SNVS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_QUERY": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_REHEADER": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_SORT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_SORT_TRGT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_STATS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_VIEW": {
+                    "bcftools": 1.2
+                },
+                "BEDTOOLS_MERGE": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_SORT": {
+                    "bedtools": "2.31.1"
+                },
+                "COMPRESS_STRANGER": {
+                    "bcftools": 1.2
+                },
+                "CRAMINO": {
+                    "cramino": "0.14.5"
+                },
+                "CRAMINO_PHASED": {
+                    "cramino": "0.14.5"
+                },
+                "CREATE_SAMPLES_FILE": {
+                    "gawk": "5.1.0"
+                },
+                "DEEPVARIANT_RUNDEEPVARIANT": {
+                    "deepvariant": "1.6.1"
+                },
+                "DEEPVARIANT_VCFSTATSREPORT": {
+                    "deepvariant": "1.6.1"
+                },
+                "DIPCALL": {
+                    "dipcall": 0.3
+                },
+                "ECHTVAR_ANNO": {
+                    "echtvar": "0.2.0"
+                },
+                "ENSEMBLVEP_FILTERVEP": {
+                    "ensemblvep": 113.0
+                },
+                "ENSEMBLVEP_SNV": {
+                    "ensemblvep": 110.0
+                },
+                "ENSEMBLVEP_SV": {
+                    "ensemblvep": 110.0
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "GENMOD_ANNOTATE": {
+                    "genmod": 3.9
+                },
+                "GENMOD_COMPOUND": {
+                    "genmod": 3.9
+                },
+                "GENMOD_MODELS": {
+                    "genmod": 3.9
+                },
+                "GENMOD_SCORE": {
+                    "genmod": 3.9
+                },
+                "GFASTATS_MATERNAL": {
+                    "gfastats": "1.3.6"
+                },
+                "GFASTATS_PATERNAL": {
+                    "gfastats": "1.3.6"
+                },
+                "GLNEXUS": {
+                    "glnexus": "1.4.3-0-gcecf42e"
+                },
+                "GUNZIP_FASTA": {
+                    "gunzip": 1.1
+                },
+                "HIFIASM": {
+                    "hifiasm": "0.20.0-r639"
+                },
+                "HIFICNV": {
+                    "hificnv": "1.0.0-36e6461"
+                },
+                "LONGPHASE_HAPLOTAG": {
+                    "longphase": "1.7.3"
+                },
+                "LONGPHASE_PHASE": {
+                    "longphase": "1.7.3"
+                },
+                "MINIMAP2_ALIGN": {
+                    "minimap2": "2.28-r1209",
+                    "samtools": 1.2
+                },
+                "MINIMAP2_INDEX": {
+                    "minimap2": "2.28-r1209"
+                },
+                "MINIMAP2_INDEX_DIPCALL": {
+                    "minimap2": "2.28-r1209"
+                },
+                "MODKIT_PILEUP": {
+                    "modkit": "0.3.0"
+                },
+                "MOSDEPTH": {
+                    "mosdepth": "0.3.8"
+                },
+                "PARAPHASE": {
+                    "minimap2": "2.28-r1209",
+                    "paraphase": "3.1.1",
+                    "samtools": 1.2
+                },
+                "RELATE_RELATE": {
+                    "somalier": "0.2.18"
+                },
+                "SAMPLESHEET_PED": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_IMPORT": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_DIPCALL": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_LONGPHASE": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_TRGT": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_MERGE": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_SORT_TRGT": {
+                    "samtools": 1.21
+                },
+                "SEVERUS": {
+                    "severus": 1.1
+                },
+                "SOMALIER_EXTRACT": {
+                    "somalier": "0.2.18"
+                },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SPLITUBAM": {
+                    "splitubam": "0.1.1"
+                },
+                "SPLIT_BED_CHUNKS": {
+                    "split_bed_chunks": 1.0
+                },
+                "STRANGER": {
+                    "stranger": "0.9.2"
+                },
+                "SVDB_MERGE": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_MERGE_SVS_CNVS": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_QUERY": {
+                    "svdb": "2.8.2"
+                },
+                "TABIX_BGZIPTABIX": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SNV": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SV": {
+                    "tabix": 1.2
+                },
+                "TABIX_LONGPHASE_PHASE": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE_SVS_CNVS": {
+                    "tabix": 1.2
+                },
+                "TABIX_TABIX": {
+                    "tabix": 1.2
+                },
+                "TRGT_GENOTYPE": {
+                    "trgt": "1.2.0-9eda4dd"
+                },
+                "TRGT_MERGE": {
+                    "trgt": "1.2.0-9eda4dd"
+                },
+                "UNTAR_VEP_CACHE": {
+                    "untar": 1.34
+                },
+                "WHATSHAP_STATS": {
+                    "whatshap": 2.3
+                },
+                "Workflow": {
+                    "genomic-medicine-sweden/nallo": "v0.4.0"
+                }
+            },
+            [
+                "aligned_reads",
+                "aligned_reads/HG002_Revio",
+                "aligned_reads/HG002_Revio/HG002_Revio_haplotagged.bam",
+                "aligned_reads/HG002_Revio/HG002_Revio_haplotagged.bam.bai",
+                "assembly_haplotypes",
+                "assembly_haplotypes/gfastats",
+                "assembly_haplotypes/gfastats/HG002_Revio",
+                "assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz",
+                "assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio/HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz",
+                "assembly_variant_calling",
+                "assembly_variant_calling/dipcall",
+                "assembly_variant_calling/dipcall/HG002_Revio",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.dip.vcf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap2.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.pair.vcf.gz",
+                "methylation",
+                "methylation/modkit",
+                "methylation/modkit/pileup",
+                "methylation/modkit/pileup/HG002_Revio",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_1.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_1.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_2.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_2.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_ungrouped.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/bcftools-stats-subtypes.txt",
+                "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
+                "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/mosdepth-coverage-per-contig-multi.txt",
+                "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt",
+                "multiqc/multiqc_data/mosdepth_cov_dist.txt",
+                "multiqc/multiqc_data/mosdepth_cumcov_dist.txt",
+                "multiqc/multiqc_data/mosdepth_perchrom.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_bcftools_stats.txt",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_somalier.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_data/multiqc_whatshap_phased_bp_plot.txt",
+                "multiqc/multiqc_data/multiqc_whatshap_stats.txt",
+                "multiqc/multiqc_data/somalier_het_check_plot.txt",
+                "multiqc/multiqc_data/somalier_sex_check_plot.txt",
+                "multiqc/multiqc_data/somalier_stats.txt",
+                "multiqc/multiqc_data/whatshap-stats-table.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-log.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf",
+                "multiqc/multiqc_plots/pdf/multiqc_whatshap_phased_bp_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_het_check_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_sex_check_plot.pdf",
+                "multiqc/multiqc_plots/pdf/whatshap-stats-table.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png",
+                "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-cnt.png",
+                "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-log.png",
+                "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png",
+                "multiqc/multiqc_plots/png/multiqc_whatshap_phased_bp_plot.png",
+                "multiqc/multiqc_plots/png/somalier_het_check_plot.png",
+                "multiqc/multiqc_plots/png/somalier_sex_check_plot.png",
+                "multiqc/multiqc_plots/png/whatshap-stats-table.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg",
+                "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg",
+                "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg",
+                "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
+                "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
+                "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
+                "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-cnt.svg",
+                "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-log.svg",
+                "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg",
+                "multiqc/multiqc_plots/svg/multiqc_whatshap_phased_bp_plot.svg",
+                "multiqc/multiqc_plots/svg/somalier_het_check_plot.svg",
+                "multiqc/multiqc_plots/svg/somalier_sex_check_plot.svg",
+                "multiqc/multiqc_plots/svg/whatshap-stats-table.svg",
+                "multiqc/multiqc_report.html",
+                "paraphase",
+                "paraphase/HG002_Revio",
+                "paraphase/HG002_Revio/HG002_Revio.paraphase.bam",
+                "paraphase/HG002_Revio/HG002_Revio.paraphase.bam.bai",
+                "paraphase/HG002_Revio/HG002_Revio.paraphase.json",
+                "paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs",
+                "paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz",
+                "paraphase/HG002_Revio/HG002_Revio_paraphase_vcfs/HG002_Revio_hba.vcf.gz.tbi",
+                "pedigree",
+                "pedigree/family",
+                "pedigree/family/FAM.ped",
+                "phased_variants",
+                "phased_variants/HG002_Revio",
+                "phased_variants/HG002_Revio/HG002_Revio_phased.vcf.gz",
+                "phased_variants/HG002_Revio/HG002_Revio_phased.vcf.gz.tbi",
+                "pipeline_info",
+                "pipeline_info/nallo_pipeline_software_mqc_versions.yml",
+                "qc",
+                "qc/cramino",
+                "qc/cramino/phased",
+                "qc/cramino/phased/HG002_Revio",
+                "qc/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.arrow",
+                "qc/cramino/phased/HG002_Revio/HG002_Revio_cramino_aligned_phased.txt",
+                "qc/cramino/unphased",
+                "qc/cramino/unphased/HG002_Revio",
+                "qc/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.arrow",
+                "qc/cramino/unphased/HG002_Revio/HG002_Revio_cramino_aligned.txt",
+                "qc/deepvariant_vcfstatsreport",
+                "qc/deepvariant_vcfstatsreport/HG002_Revio",
+                "qc/deepvariant_vcfstatsreport/HG002_Revio/HG002_Revio.visual_report.html",
+                "qc/fastqc",
+                "qc/fastqc/HG002_Revio",
+                "qc/fastqc/HG002_Revio/HG002_Revio_fastqc.html",
+                "qc/fastqc/HG002_Revio/HG002_Revio_fastqc.zip",
+                "qc/mosdepth",
+                "qc/mosdepth/HG002_Revio",
+                "qc/mosdepth/HG002_Revio/HG002_Revio.mosdepth.global.dist.txt",
+                "qc/mosdepth/HG002_Revio/HG002_Revio.mosdepth.region.dist.txt",
+                "qc/mosdepth/HG002_Revio/HG002_Revio.mosdepth.summary.txt",
+                "qc/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz",
+                "qc/mosdepth/HG002_Revio/HG002_Revio.regions.bed.gz.csi",
+                "qc/phasing_stats",
+                "qc/phasing_stats/HG002_Revio",
+                "qc/phasing_stats/HG002_Revio/HG002_Revio_stats.blocks.tsv",
+                "qc/phasing_stats/HG002_Revio/HG002_Revio_stats.stats.tsv",
+                "qc/somalier",
+                "qc/somalier/relate",
+                "qc/somalier/relate/test",
+                "qc/somalier/relate/test/test.html",
+                "qc/somalier/relate/test/test.pairs.tsv",
+                "qc/somalier/relate/test/test.samples.tsv",
+                "repeats",
+                "repeats/family",
+                "repeats/family/FAM",
+                "repeats/family/FAM/FAM_repeats_annotated.vcf.gz",
+                "repeats/family/FAM/FAM_repeats_annotated.vcf.gz.tbi",
+                "repeats/sample",
+                "repeats/sample/HG002_Revio",
+                "repeats/sample/HG002_Revio/HG002_Revio_sorted.vcf.gz",
+                "repeats/sample/HG002_Revio/HG002_Revio_sorted.vcf.gz.tbi",
+                "repeats/sample/HG002_Revio/HG002_Revio_spanning_sorted.bam",
+                "repeats/sample/HG002_Revio/HG002_Revio_spanning_sorted.bam.bai",
+                "snvs",
+                "snvs/family",
+                "snvs/family/FAM",
+                "snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz",
+                "snvs/family/FAM/FAM_snv_annotated_ranked.vcf.gz.tbi",
+                "snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz",
+                "snvs/family/FAM/FAM_snvs_annotated_ranked_filtered.vcf.gz.tbi",
+                "snvs/sample",
+                "snvs/sample/HG002_Revio",
+                "snvs/sample/HG002_Revio/HG002_Revio_snvs_annotated_ranked.vcf.gz",
+                "snvs/sample/HG002_Revio/HG002_Revio_snvs_annotated_ranked.vcf.gz.tbi",
+                "snvs/stats",
+                "snvs/stats/sample",
+                "snvs/stats/sample/HG002_Revio.vcf.gz.bcftools_stats.txt",
+                "svs",
+                "svs/family",
+                "svs/family/FAM",
+                "svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
+                "svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked.vcf.gz.tbi",
+                "svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz",
+                "svs/family/FAM/FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz.tbi",
+                "svs/sample",
+                "svs/sample/HG002_Revio",
+                "svs/sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz",
+                "svs/sample/HG002_Revio/HG002_Revio_cnvs.vcf.gz.tbi",
+                "svs/sample/HG002_Revio/HG002_Revio_svs.vcf.gz",
+                "svs/sample/HG002_Revio/HG002_Revio_svs.vcf.gz.tbi",
+                "visualization_tracks",
+                "visualization_tracks/HG002_Revio",
+                "visualization_tracks/HG002_Revio/HG002_Revio_hificnv.copynum.bedgraph",
+                "visualization_tracks/HG002_Revio/HG002_Revio_hificnv.depth.bw",
+                "visualization_tracks/HG002_Revio/HG002_Revio_hificnv.maf.bw"
+            ],
+            [
+                "HG002_Revio.asm.bp.hap1.p_ctg.assembly_summary:md5,b949217515292b5a7735af4ad4bd5b11",
+                "HG002_Revio.asm.bp.hap1.p_ctg.fasta.gz:md5,380ed173f8d50419a86c229dd81a20c2",
+                "HG002_Revio.asm.bp.hap2.p_ctg.assembly_summary:md5,c3e50f54e9e2871771d1735c54e57c5e",
+                "HG002_Revio.asm.bp.hap2.p_ctg.fasta.gz:md5,6ca4cd66b46b2bf7b1ed1ee959fba6ab",
+                "HG002_Revio.dip.bed:md5,8230ffcc5539eef359ab5128fa60e765",
+                "HG002_Revio.dip.vcf.gz:md5,747ea6c9532679ae7eb5ce06f511c4c2",
+                "HG002_Revio.hap1.bam:md5,91467717def7554e5ed667a103b52ebb",
+                "HG002_Revio.hap1.bam.bai:md5,3d7137693801619c4afb4cb493c35d40",
+                "HG002_Revio.hap1.bed:md5,44dcedabe0edb29af441df1f0b55210a",
+                "HG002_Revio.hap1.paf.gz:md5,680a7278a2d492ed6ee5c7b19dd5d80f",
+                "HG002_Revio.hap1.sam.gz:md5,87781cea76b064c23d1b63a34423b23f",
+                "HG002_Revio.hap1.var.gz:md5,bd714e935825d8c665445d93c7d82206",
+                "HG002_Revio.hap2.bam:md5,f1da738bd01db5c6e5e8b18906fe30f2",
+                "HG002_Revio.hap2.bam.bai:md5,04a41250610872ae3bf86108be610883",
+                "HG002_Revio.hap2.bed:md5,6b4b879d4ebe97f778921252469a029c",
+                "HG002_Revio.hap2.paf.gz:md5,77ff9e7c1b0ed8454f7a10beba01cbf9",
+                "HG002_Revio.hap2.sam.gz:md5,6d512a060c74428f7758aa51a99ae8c8",
+                "HG002_Revio.hap2.var.gz:md5,9ba9303b30730e419138e177c7d1e0c2",
+                "HG002_Revio.pair.vcf.gz:md5,1909dffa43850282fe7e5ae2b2d273a7",
+                "HG002_Revio_modkit_pileup_1.bed.gz:md5,ac9bfc455d0b697a4bd565b510c155e0",
+                "HG002_Revio_modkit_pileup_1.bed.gz.tbi:md5,5a9ac375a0ce33af002e0073635a3425",
+                "HG002_Revio_modkit_pileup_2.bed.gz:md5,b2c6c3fc27d34b7c588a4a4b3e9611b0",
+                "HG002_Revio_modkit_pileup_2.bed.gz.tbi:md5,2ad55c2f604cbdf6a784b2dd99b25cb1",
+                "HG002_Revio_modkit_pileup_ungrouped.bed.gz:md5,04ee840c02e04238b9432bc374a1afe1",
+                "HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi:md5,e1418c8075da8831a52e0cd56ceb910e",
+                "bcftools-stats-subtypes.txt:md5,2c23b13117d584b4f424c2bc56dfa4ba",
+                "bcftools_stats_indel-lengths.txt:md5,bea599c38615af6a033ea3a4436d52c5",
+                "fastqc-status-check-heatmap.txt:md5,f98c3e5395cfd3061b3228a97ba86043",
+                "fastqc_adapter_content_plot.txt:md5,85e76640241ce1fd8e3bbf42eb3fa447",
+                "fastqc_per_base_n_content_plot.txt:md5,c9e46e2888289c319e1b9f412cb0d8e5",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,6900fc0ad6d05cc49412c9a169473ea8",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,4f7571e0b1ef7c917054325aff07d96f",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,70bb2678985be387db93805d5e9fbf2f",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,f45a447b91a80e8c6d69607057c828fa",
+                "fastqc_sequence_counts_plot.txt:md5,464423ea1a9c9db427b47df6f441c079",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3da083f3e5e3c37d8ba3d766c5ef2b85",
+                "fastqc_sequence_length_distribution_plot.txt:md5,014a4c2dbe604408e7b0c359252016f1",
+                "fastqc_top_overrepresented_sequences_table.txt:md5,21d4be95f2fc981c3f5f8fbe1855bf53",
+                "mosdepth-coverage-per-contig-multi.txt:md5,39f24c236ea9413f3835ddf24eea86a8",
+                "mosdepth-cumcoverage-dist-id.txt:md5,ae88f53eaadf28d333f1fbd490d38725",
+                "mosdepth_cov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413",
+                "mosdepth_cumcov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413",
+                "mosdepth_perchrom.txt:md5,53806d793d5627e60648daebb6606723",
+                "multiqc_bcftools_stats.txt:md5,09a616618fb506994ce178d32325159f",
+                "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
+                "multiqc_fastqc.txt:md5,8c0330b85e73f68610d35dd71f234cce",
+                "multiqc_general_stats.txt:md5,8ead46d7d8d14fc8892789a40193646f",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,41dcd2951f7a6f925f64519491c18d45",
+                "multiqc_whatshap_stats.txt:md5,c8c212ecc6fbf6803f8de87f2395363f",
+                "somalier_stats.txt:md5,150fa6b9c197c539947168c11d2115f9",
+                "whatshap-stats-table.txt:md5,c89df1fe6abe77dcbfce8e443c1cecde",
+                "FAM.ped:md5,bd5cec27ba7337a85cf98e787131e2b5",
+                "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                "HG002_Revio.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
+                "HG002_Revio.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
+                "HG002_Revio.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
+                "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
+                "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
+                "HG002_Revio_stats.blocks.tsv:md5,e73960d863a78848498499480ea9937f",
+                "HG002_Revio_stats.stats.tsv:md5,cffa4a500350b2227ab40bbbe428e9ef",
+                "HG002_Revio_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
+                "HG002_Revio_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
+                "HG002_Revio_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c"
+            ],
+            [
+                [
+                    "HG002_Revio_haplotagged.bam",
+                    "3367d07489e728a2a99d9abb618841ec"
+                ],
+                [
+                    "HG002_Revio.hap1.bam",
+                    "da103c401cf854a00aa75a57cda0f34d"
+                ],
+                [
+                    "HG002_Revio.hap2.bam",
+                    "e8599cef23fc88e2fe09d2bda5ea372f"
+                ],
+                [
+                    "HG002_Revio.paraphase.bam",
+                    "fcc3f220bb09d3264f97e7f620779be0"
+                ],
+                [
+                    "HG002_Revio_spanning_sorted.bam",
+                    "a51f00198c7449fd64772fe680c6241"
+                ]
+            ],
+            [
+                [
+                    "HG002_Revio.dip.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=1917, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio.pair.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=1917, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_hba.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=2121, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_phased.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=191, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_repeats_annotated.vcf.gz",
+                    "VcfFile [chromosomes=[chr20], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_sorted.vcf.gz",
+                    "VcfFile [chromosomes=[chr20], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snv_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=103, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snvs_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_snvs_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=87, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_cnvs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_svs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                [
+                    "HG002_Revio.dip.vcf.gz",
+                    "db10cdb233cb09a46c1694536c2e79e7"
+                ],
+                [
+                    "HG002_Revio.pair.vcf.gz",
+                    "fa3bfacdab5449526d29d642340d6708"
+                ],
+                [
+                    "FAM_repeats_annotated.vcf.gz",
+                    "c70a3906d95d9d9c0a1a61c354302c7c"
+                ],
+                [
+                    "HG002_Revio_sorted.vcf.gz",
+                    "d7d518f68789d3d51a26be28a93b9654"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T15:33:19.851771321"
+    }
+}
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_bam.nf.test b/tests/samplesheet_multisample_bam.nf.test
new file mode 100644
index 00000000..3099f149
--- /dev/null
+++ b/tests/samplesheet_multisample_bam.nf.test
@@ -0,0 +1,53 @@
+nextflow_pipeline {
+
+    name "Test pipeline GENOMICMEDICINESWEDEN_NALLO"
+    script "../main.nf"
+    tag "PIPELINE"
+
+    test("samplesheet_multisample_bam | --phaser hiphase") {
+        tag "samplesheet_multisample_bam"
+
+        when {
+            params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
+                input                        = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam.csv'
+                outdir                       = "$outputDir"
+                phaser                       = "hiphase"
+
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name      = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path      = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files        = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            // all_vcf_files: All vcf files - can have unstable variants and/or unstable headers
+            def all_vcf_files    = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
+            // stable_vcf_files: Vcf files with stable variants - can be snapshot unsing variantsMD5
+            def stable_vcf_files = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore_unstable_variants', include: ['**/*.vcf.gz'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nallo_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString(), stringency: 'silent').getReadsMD5() ] },
+                    // All vcf files
+                    all_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.summary ] },
+                    // Stable vcf files
+                    stable_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5 ] }
+                ).match() }
+            )
+        }
+    }
+
+}
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
new file mode 100644
index 00000000..6a6c10e0
--- /dev/null
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -0,0 +1,877 @@
+{
+    "samplesheet_multisample_bam | --phaser hiphase": {
+        "content": [
+            159,
+            {
+                "ADD_FOUND_IN_TAG": {
+                    "bcftools": 1.2,
+                    "busybox_awk": "1.36.1"
+                },
+                "ADD_MOST_SEVERE_CSQ": {
+                    "add_most_severe_consequence": 1.0,
+                    "python": "3.8.3"
+                },
+                "ADD_MOST_SEVERE_PLI": {
+                    "add_most_severe_pli": 1.0,
+                    "python": "3.8.3"
+                },
+                "BCFTOOLS_CONCAT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS_ANNO": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_INDEX": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_MULTISAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_SINGLESAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_PLUGINSPLIT_SNVS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_QUERY": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_REHEADER": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_SORT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_SORT_TRGT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_STATS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_VIEW": {
+                    "bcftools": 1.2
+                },
+                "BEDTOOLS_MERGE": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_SORT": {
+                    "bedtools": "2.31.1"
+                },
+                "COMPRESS_STRANGER": {
+                    "bcftools": 1.2
+                },
+                "CRAMINO": {
+                    "cramino": "0.14.5"
+                },
+                "CRAMINO_PHASED": {
+                    "cramino": "0.14.5"
+                },
+                "CREATE_SAMPLES_FILE": {
+                    "gawk": "5.1.0"
+                },
+                "DEEPVARIANT_RUNDEEPVARIANT": {
+                    "deepvariant": "1.6.1"
+                },
+                "DEEPVARIANT_VCFSTATSREPORT": {
+                    "deepvariant": "1.6.1"
+                },
+                "DIPCALL": {
+                    "dipcall": 0.3
+                },
+                "ECHTVAR_ANNO": {
+                    "echtvar": "0.2.0"
+                },
+                "ENSEMBLVEP_FILTERVEP": {
+                    "ensemblvep": 113.0
+                },
+                "ENSEMBLVEP_SNV": {
+                    "ensemblvep": 110.0
+                },
+                "ENSEMBLVEP_SV": {
+                    "ensemblvep": 110.0
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "GENMOD_ANNOTATE": {
+                    "genmod": 3.9
+                },
+                "GENMOD_COMPOUND": {
+                    "genmod": 3.9
+                },
+                "GENMOD_MODELS": {
+                    "genmod": 3.9
+                },
+                "GENMOD_SCORE": {
+                    "genmod": 3.9
+                },
+                "GFASTATS_MATERNAL": {
+                    "gfastats": "1.3.6"
+                },
+                "GFASTATS_PATERNAL": {
+                    "gfastats": "1.3.6"
+                },
+                "GLNEXUS": {
+                    "glnexus": "1.4.3-0-gcecf42e"
+                },
+                "GUNZIP_FASTA": {
+                    "gunzip": 1.1
+                },
+                "HIFIASM": {
+                    "hifiasm": "0.20.0-r639"
+                },
+                "HIFICNV": {
+                    "hificnv": "1.0.0-36e6461"
+                },
+                "HIPHASE": {
+                    "hiphase": "1.4.0-7bf2743"
+                },
+                "MINIMAP2_ALIGN": {
+                    "minimap2": "2.28-r1209",
+                    "samtools": 1.2
+                },
+                "MINIMAP2_INDEX": {
+                    "minimap2": "2.28-r1209"
+                },
+                "MINIMAP2_INDEX_DIPCALL": {
+                    "minimap2": "2.28-r1209"
+                },
+                "MODKIT_PILEUP": {
+                    "modkit": "0.3.0"
+                },
+                "MOSDEPTH": {
+                    "mosdepth": "0.3.8"
+                },
+                "PARAPHASE": {
+                    "minimap2": "2.28-r1209",
+                    "paraphase": "3.1.1",
+                    "samtools": 1.2
+                },
+                "RELATE_INFER": {
+                    "somalier": "0.2.18"
+                },
+                "RELATE_RELATE": {
+                    "somalier": "0.2.18"
+                },
+                "SAMPLESHEET_PED": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_FASTQ": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_DIPCALL": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_TRGT": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_MERGE": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_SORT_TRGT": {
+                    "samtools": 1.21
+                },
+                "SEVERUS": {
+                    "severus": 1.1
+                },
+                "SOMALIER_EXTRACT": {
+                    "somalier": "0.2.18"
+                },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SPLITUBAM": {
+                    "splitubam": "0.1.1"
+                },
+                "SPLIT_BED_CHUNKS": {
+                    "split_bed_chunks": 1.0
+                },
+                "STRANGER": {
+                    "stranger": "0.9.2"
+                },
+                "SVDB_MERGE": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_MERGE_SVS_CNVS": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_QUERY": {
+                    "svdb": "2.8.2"
+                },
+                "TABIX_BGZIPTABIX": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SNV": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SV": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE_SVS_CNVS": {
+                    "tabix": 1.2
+                },
+                "TABIX_TABIX": {
+                    "tabix": 1.2
+                },
+                "TRGT_GENOTYPE": {
+                    "trgt": "1.2.0-9eda4dd"
+                },
+                "TRGT_MERGE": {
+                    "trgt": "1.2.0-9eda4dd"
+                },
+                "UNTAR_VEP_CACHE": {
+                    "untar": 1.34
+                },
+                "WHATSHAP_STATS": {
+                    "whatshap": 2.3
+                },
+                "Workflow": {
+                    "genomic-medicine-sweden/nallo": "v0.4.0"
+                }
+            },
+            [
+                "aligned_reads",
+                "aligned_reads/HG002_Revio_A",
+                "aligned_reads/HG002_Revio_A/HG002_Revio_A_haplotagged.bam",
+                "aligned_reads/HG002_Revio_A/HG002_Revio_A_haplotagged.bam.bai",
+                "aligned_reads/HG002_Revio_B",
+                "aligned_reads/HG002_Revio_B/HG002_Revio_B_haplotagged.bam",
+                "aligned_reads/HG002_Revio_B/HG002_Revio_B_haplotagged.bam.bai",
+                "assembly_haplotypes",
+                "assembly_haplotypes/gfastats",
+                "assembly_haplotypes/gfastats/HG002_Revio_A",
+                "assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap1.p_ctg.fasta.gz",
+                "assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio_A/HG002_Revio_A.asm.bp.hap2.p_ctg.fasta.gz",
+                "assembly_haplotypes/gfastats/HG002_Revio_B",
+                "assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap1.p_ctg.fasta.gz",
+                "assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.assembly_summary",
+                "assembly_haplotypes/gfastats/HG002_Revio_B/HG002_Revio_B.asm.bp.hap2.p_ctg.fasta.gz",
+                "assembly_variant_calling",
+                "assembly_variant_calling/dipcall",
+                "assembly_variant_calling/dipcall/HG002_Revio_A",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.dip.vcf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap1.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.hap2.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_A/HG002_Revio_A.pair.vcf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.dip.vcf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bam.bai",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.bed",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.paf.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.sam.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap2.var.gz",
+                "assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.pair.vcf.gz",
+                "methylation",
+                "methylation/modkit",
+                "methylation/modkit/pileup",
+                "methylation/modkit/pileup/HG002_Revio_A",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_1.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_1.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_2.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_2.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_ungrouped.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_A/HG002_Revio_A_modkit_pileup_ungrouped.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio_B",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_1.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_1.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_2.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_2.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_ungrouped.bed.gz",
+                "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/bcftools-stats-subtypes.txt",
+                "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
+                "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
+                "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/mosdepth-coverage-per-contig-multi.txt",
+                "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt",
+                "multiqc/multiqc_data/mosdepth_cov_dist.txt",
+                "multiqc/multiqc_data/mosdepth_cumcov_dist.txt",
+                "multiqc/multiqc_data/mosdepth_perchrom.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_bcftools_stats.txt",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_somalier.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_data/multiqc_whatshap_phased_bp_plot.txt",
+                "multiqc/multiqc_data/multiqc_whatshap_stats.txt",
+                "multiqc/multiqc_data/somalier_het_check_plot.txt",
+                "multiqc/multiqc_data/somalier_relatedness_heatmap_plot.txt",
+                "multiqc/multiqc_data/somalier_relatedness_plot.txt",
+                "multiqc/multiqc_data/somalier_sex_check_plot.txt",
+                "multiqc/multiqc_data/somalier_stats.txt",
+                "multiqc/multiqc_data/whatshap-stats-table.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
+                "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-log.pdf",
+                "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf",
+                "multiqc/multiqc_plots/pdf/multiqc_whatshap_phased_bp_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_het_check_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_relatedness_heatmap_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_relatedness_plot.pdf",
+                "multiqc/multiqc_plots/pdf/somalier_sex_check_plot.pdf",
+                "multiqc/multiqc_plots/pdf/whatshap-stats-table.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png",
+                "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
+                "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-cnt.png",
+                "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-log.png",
+                "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png",
+                "multiqc/multiqc_plots/png/multiqc_whatshap_phased_bp_plot.png",
+                "multiqc/multiqc_plots/png/somalier_het_check_plot.png",
+                "multiqc/multiqc_plots/png/somalier_relatedness_heatmap_plot.png",
+                "multiqc/multiqc_plots/png/somalier_relatedness_plot.png",
+                "multiqc/multiqc_plots/png/somalier_sex_check_plot.png",
+                "multiqc/multiqc_plots/png/whatshap-stats-table.png",
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+                "mosdepth_cumcov_dist.txt:md5,c53933e0b572d115ecd35a5adb3e0a04",
+                "mosdepth_perchrom.txt:md5,9fd9c40c7a6be06a338f2039a5d91fb8",
+                "multiqc_bcftools_stats.txt:md5,dbbc176792fbf2845547dfdcd39fc208",
+                "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
+                "multiqc_fastqc.txt:md5,e466de366de86998b84ba6c25aafafd6",
+                "multiqc_general_stats.txt:md5,d1bfae61713bed6068386db5cb92cde9",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,d70d629693c3229c37750440636c0a90",
+                "multiqc_whatshap_stats.txt:md5,96447de4e14a9b4a570c24513de64970",
+                "somalier_stats.txt:md5,5f523bdaa8f6b6bf1581694564521891",
+                "whatshap-stats-table.txt:md5,862f90185133703811c955c45f5750fa",
+                "FAM.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4",
+                "HG002_Revio_A_phased.blocks.tsv:md5,27ce044ba581da15ef838cbb343a64cf",
+                "HG002_Revio_A_phased.stats.tsv:md5,58ae1b01d01b922d022ad025a81f1026",
+                "HG002_Revio_A_phased.summary.tsv:md5,714496292cba53669081ac3be3078c28",
+                "HG002_Revio_B_phased.blocks.tsv:md5,07e7c8ebfff969db8d16890aa6a4766b",
+                "HG002_Revio_B_phased.stats.tsv:md5,f5d83609c032dee6d3056559a5994b15",
+                "HG002_Revio_B_phased.summary.tsv:md5,4acacb1a89a27ddf4c4ca49c49899245",
+                "HG002_Revio_A_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                "HG002_Revio_B_cramino_aligned_phased.arrow:md5,544a6513e7604d6425a664855212eced",
+                "HG002_Revio_A_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
+                "HG002_Revio_B_cramino_aligned.arrow:md5,544a6513e7604d6425a664855212eced",
+                "HG002_Revio_A.mosdepth.global.dist.txt:md5,6186315d4d65eda85553af82a98829d1",
+                "HG002_Revio_A.mosdepth.region.dist.txt:md5,c6c7ee8f056b8b2b92c97ec472b1db16",
+                "HG002_Revio_A.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
+                "HG002_Revio_A.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
+                "HG002_Revio_A.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
+                "HG002_Revio_B.mosdepth.global.dist.txt:md5,830a8b737fea939dcfea4d1626e60576",
+                "HG002_Revio_B.mosdepth.region.dist.txt:md5,d4cb66ac28dc6816869a73757226f902",
+                "HG002_Revio_B.mosdepth.summary.txt:md5,191877ae5228e7880276585557a7b218",
+                "HG002_Revio_B.regions.bed.gz:md5,9c4c037139c752c60385d3c0b905af7f",
+                "HG002_Revio_B.regions.bed.gz.csi:md5,d0640255d527e36655281f64e184b02c",
+                "HG002_Revio_A_stats.blocks.tsv:md5,846f21bc3d8dd9e9d68cb00d63484ec2",
+                "HG002_Revio_A_stats.stats.tsv:md5,1504949804b510cc57d20e2c78fb7294",
+                "HG002_Revio_B_stats.blocks.tsv:md5,df646f43e67f37df5a9ec148e431d4c3",
+                "HG002_Revio_B_stats.stats.tsv:md5,40994b57e7c0bafee411bc2ad6ffb79d",
+                "HG002_Revio_A_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
+                "HG002_Revio_A_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
+                "HG002_Revio_A_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c",
+                "HG002_Revio_B_hificnv.copynum.bedgraph:md5,42095da173e46804977bbbecc2fda3aa",
+                "HG002_Revio_B_hificnv.depth.bw:md5,f49416b122b334f3defe7bee6dd60d48",
+                "HG002_Revio_B_hificnv.maf.bw:md5,186a7500b0c039650f726480e44b621d"
+            ],
+            [
+                [
+                    "HG002_Revio_A_haplotagged.bam",
+                    "74b4822241bd8d1bc42f494f1f3e326c"
+                ],
+                [
+                    "HG002_Revio_B_haplotagged.bam",
+                    "4fc125e25365fa6e33193fd436ae135d"
+                ],
+                [
+                    "HG002_Revio_A.hap1.bam",
+                    "da103c401cf854a00aa75a57cda0f34d"
+                ],
+                [
+                    "HG002_Revio_A.hap2.bam",
+                    "e8599cef23fc88e2fe09d2bda5ea372f"
+                ],
+                [
+                    "HG002_Revio_B.hap1.bam",
+                    "2352f7a9960c400d8182ad2ec442887"
+                ],
+                [
+                    "HG002_Revio_B.hap2.bam",
+                    "6e4f7fa25e9905d538ecc65f923806"
+                ],
+                [
+                    "HG002_Revio_A.paraphase.bam",
+                    "fcc3f220bb09d3264f97e7f620779be0"
+                ],
+                [
+                    "HG002_Revio_B.paraphase.bam",
+                    "fcc3f220bb09d3264f97e7f620779be0"
+                ],
+                [
+                    "HG002_Revio_A_spanning_sorted.bam",
+                    "a51f00198c7449fd64772fe680c6241"
+                ],
+                [
+                    "HG002_Revio_B_spanning_sorted.bam",
+                    "a51f00198c7449fd64772fe680c6241"
+                ]
+            ],
+            [
+                [
+                    "HG002_Revio_A.dip.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=1917, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A.pair.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=1917, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B.dip.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=1862, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B.pair.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=1862, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_hba.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=2121, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_hba.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=2121, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_phased.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=191, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_phased.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=191, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_repeats_annotated.vcf.gz",
+                    "VcfFile [chromosomes=[chr20], sampleCount=2, variantCount=2, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_sorted.vcf.gz",
+                    "VcfFile [chromosomes=[chr20], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_sorted.vcf.gz",
+                    "VcfFile [chromosomes=[chr20], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snv_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=104, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snvs_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=55, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_snvs_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_snvs_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=87, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=5, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_cnvs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_A_svs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_cnvs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=36, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_Revio_B_svs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=55, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                [
+                    "HG002_Revio_A.dip.vcf.gz",
+                    "db10cdb233cb09a46c1694536c2e79e7"
+                ],
+                [
+                    "HG002_Revio_A.pair.vcf.gz",
+                    "fa3bfacdab5449526d29d642340d6708"
+                ],
+                [
+                    "HG002_Revio_B.dip.vcf.gz",
+                    "eecfa7a0111b2ababb2e37fb91686b3f"
+                ],
+                [
+                    "HG002_Revio_B.pair.vcf.gz",
+                    "83dc2bb5d8f46bf3daf99f27e4d3b022"
+                ],
+                [
+                    "FAM_repeats_annotated.vcf.gz",
+                    "951b776cf91119f9962b75756acedbd0"
+                ],
+                [
+                    "HG002_Revio_A_sorted.vcf.gz",
+                    "d7d518f68789d3d51a26be28a93b9654"
+                ],
+                [
+                    "HG002_Revio_B_sorted.vcf.gz",
+                    "d7d518f68789d3d51a26be28a93b9654"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T15:15:01.966301935"
+    }
+}
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test b/tests/samplesheet_multisample_ont_bam.nf.test
new file mode 100644
index 00000000..826bcd65
--- /dev/null
+++ b/tests/samplesheet_multisample_ont_bam.nf.test
@@ -0,0 +1,55 @@
+nextflow_pipeline {
+
+    name "Test pipeline GENOMICMEDICINESWEDEN_NALLO"
+    script "../main.nf"
+    tag "PIPELINE"
+
+    test("samplesheet_multisample_ont_bam | --preset ONT_R10 --phaser whatshap --alignment_processes 1 --snv_calling_processes 1") {
+        tag "samplesheet_multisample_ont_bam"
+
+        when {
+            params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
+                input                        = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam_ont.csv'
+                outdir                       = "$outputDir"
+                preset                       = 'ONT_R10'
+                alignment_processes          = 1
+                snv_calling_processes        = 1
+                phaser                       = "whatshap"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name      = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path      = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files        = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            // all_vcf_files: All vcf files - can have unstable variants and/or unstable headers
+            def all_vcf_files    = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
+            // stable_vcf_files: Vcf files with stable variants - can be snapshot unsing variantsMD5
+            def stable_vcf_files = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore_unstable_variants', include: ['**/*.vcf.gz'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nallo_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString(), stringency: 'silent').getReadsMD5() ] },
+                    // All vcf files
+                    all_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.summary ] },
+                    // Stable vcf files
+                    stable_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5 ] }
+                ).match() }
+            )
+        }
+    }
+
+}
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
new file mode 100644
index 00000000..01e5e5ab
--- /dev/null
+++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -0,0 +1,643 @@
+{
+    "samplesheet_multisample_ont_bam | --preset ONT_R10 --phaser whatshap --alignment_processes 1 --snv_calling_processes 1": {
+        "content": [
+            107,
+            {
+                "ADD_FOUND_IN_TAG": {
+                    "bcftools": 1.2,
+                    "busybox_awk": "1.36.1"
+                },
+                "ADD_MOST_SEVERE_CSQ": {
+                    "add_most_severe_consequence": 1.0,
+                    "python": "3.8.3"
+                },
+                "ADD_MOST_SEVERE_PLI": {
+                    "add_most_severe_pli": 1.0,
+                    "python": "3.8.3"
+                },
+                "BCFTOOLS_CONCAT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_FILLTAGS_ANNO": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_MULTISAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_NORM_SINGLESAMPLE": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_PLUGINSPLIT_SNVS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_QUERY": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_REHEADER": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_SORT": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_STATS": {
+                    "bcftools": 1.2
+                },
+                "BCFTOOLS_VIEW": {
+                    "bcftools": 1.2
+                },
+                "BEDTOOLS_MERGE": {
+                    "bedtools": "2.31.1"
+                },
+                "BEDTOOLS_SORT": {
+                    "bedtools": "2.31.1"
+                },
+                "CRAMINO": {
+                    "cramino": "0.14.5"
+                },
+                "CRAMINO_PHASED": {
+                    "cramino": "0.14.5"
+                },
+                "CREATE_SAMPLES_FILE": {
+                    "gawk": "5.1.0"
+                },
+                "DEEPVARIANT_RUNDEEPVARIANT": {
+                    "deepvariant": "1.6.1"
+                },
+                "DEEPVARIANT_VCFSTATSREPORT": {
+                    "deepvariant": "1.6.1"
+                },
+                "ECHTVAR_ANNO": {
+                    "echtvar": "0.2.0"
+                },
+                "ENSEMBLVEP_FILTERVEP": {
+                    "ensemblvep": 113.0
+                },
+                "ENSEMBLVEP_SNV": {
+                    "ensemblvep": 110.0
+                },
+                "ENSEMBLVEP_SV": {
+                    "ensemblvep": 110.0
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "GENMOD_ANNOTATE": {
+                    "genmod": 3.9
+                },
+                "GENMOD_COMPOUND": {
+                    "genmod": 3.9
+                },
+                "GENMOD_MODELS": {
+                    "genmod": 3.9
+                },
+                "GENMOD_SCORE": {
+                    "genmod": 3.9
+                },
+                "GLNEXUS": {
+                    "glnexus": "1.4.3-0-gcecf42e"
+                },
+                "GUNZIP_FASTA": {
+                    "gunzip": 1.1
+                },
+                "HIFICNV": {
+                    "hificnv": "1.0.0-36e6461"
+                },
+                "MINIMAP2_ALIGN": {
+                    "minimap2": "2.28-r1209",
+                    "samtools": 1.2
+                },
+                "MINIMAP2_INDEX": {
+                    "minimap2": "2.28-r1209"
+                },
+                "MODKIT_PILEUP": {
+                    "modkit": "0.3.0"
+                },
+                "MOSDEPTH": {
+                    "mosdepth": "0.3.8"
+                },
+                "PARAPHASE": {
+                    "minimap2": "2.28-r1209",
+                    "paraphase": "3.1.1",
+                    "samtools": 1.2
+                },
+                "RELATE_RELATE": {
+                    "somalier": "0.2.18"
+                },
+                "SAMPLESHEET_PED": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_INDEX_WHATSHAP": {
+                    "samtools": 1.21
+                },
+                "SAMTOOLS_MERGE": {
+                    "samtools": 1.21
+                },
+                "SEVERUS": {
+                    "severus": 1.1
+                },
+                "SOMALIER_EXTRACT": {
+                    "somalier": "0.2.18"
+                },
+                "SOMALIER_PED_FAMILY": {
+                    "create_pedigree_file": 1.0,
+                    "python": "3.8.3"
+                },
+                "SPLIT_BED_CHUNKS": {
+                    "split_bed_chunks": 1.0
+                },
+                "SVDB_MERGE": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_MERGE_SVS_CNVS": {
+                    "svdb": "2.8.2",
+                    "bcftools": 1.21
+                },
+                "SVDB_QUERY": {
+                    "svdb": "2.8.2"
+                },
+                "TABIX_BGZIPTABIX": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SNV": {
+                    "tabix": 1.2
+                },
+                "TABIX_ENSEMBLVEP_SV": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE": {
+                    "tabix": 1.2
+                },
+                "TABIX_SVDB_MERGE_SVS_CNVS": {
+                    "tabix": 1.2
+                },
+                "TABIX_TABIX": {
+                    "tabix": 1.2
+                },
+                "UNTAR_VEP_CACHE": {
+                    "untar": 1.34
+                },
+                "WHATSHAP_HAPLOTAG": {
+                    "whatshap": 2.3
+                },
+                "WHATSHAP_PHASE": {
+                    "whatshap": 2.3,
+                    "bgzip": 1.2,
+                    "tabix": 1.2
+                },
+                "WHATSHAP_STATS": {
+                    "whatshap": 2.3
+                },
+                "Workflow": {
+                    "genomic-medicine-sweden/nallo": "v0.4.0"
+                }
+            },
+            [
+                "aligned_reads",
+                "aligned_reads/HG002_ONT_A",
+                "aligned_reads/HG002_ONT_A/HG002_ONT_A_haplotagged.bam",
+                "aligned_reads/HG002_ONT_A/HG002_ONT_A_haplotagged.bam.bai",
+                "aligned_reads/HG002_ONT_B",
+                "aligned_reads/HG002_ONT_B/HG002_ONT_B_haplotagged.bam",
+                "aligned_reads/HG002_ONT_B/HG002_ONT_B_haplotagged.bam.bai",
+                "methylation",
+                "methylation/modkit",
+                "methylation/modkit/pileup",
+                "methylation/modkit/pileup/HG002_ONT_A",
+                "methylation/modkit/pileup/HG002_ONT_A/HG002_ONT_A_modkit_pileup_1.bed.gz",
+                "methylation/modkit/pileup/HG002_ONT_A/HG002_ONT_A_modkit_pileup_1.bed.gz.tbi",
+                "methylation/modkit/pileup/HG002_ONT_A/HG002_ONT_A_modkit_pileup_2.bed.gz",
+                "methylation/modkit/pileup/HG002_ONT_A/HG002_ONT_A_modkit_pileup_2.bed.gz.tbi",
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+                "bcftools_stats_indel-lengths.txt:md5,cc976b96114f0b68daffec58a7643d53",
+                "fastqc-status-check-heatmap.txt:md5,03e5dc3abd2f2599a7bb03739dd5ca86",
+                "fastqc_adapter_content_plot.txt:md5,00c7bec7dd9304848f7d891d7d1fab7f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,6f0148406e9d5358bf37375b33a4bc01",
+                "fastqc_per_base_n_content_plot.txt:md5,8551be865db8162f7d6203e0e34288e0",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,f5e2e866bebda66cd877522342a2bf8a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8f108751cb49e0d80729247b84ddee76",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,2c68289482d7bffc37efe8110eff9328",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,eb18c5356c9bf4eae99f0103b04a8a81",
+                "fastqc_sequence_counts_plot.txt:md5,d80ddc5d3e3810f5bad4e04b85bd3056",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,005e3c05e83b9e681f7d02709007df15",
+                "fastqc_sequence_length_distribution_plot.txt:md5,befaab9e643f27b4fc184577e2dd9dda",
+                "fastqc_top_overrepresented_sequences_table.txt:md5,48a5253938a61c69babe90a5c7c4b862",
+                "mosdepth-coverage-per-contig-multi.txt:md5,4339c1147fa7ec9059126bf4c8b6760e",
+                "mosdepth-cumcoverage-dist-id.txt:md5,d18aa3d23b90333c6d6d84bd0510c5c6",
+                "mosdepth_cov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9",
+                "mosdepth_cumcov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9",
+                "mosdepth_perchrom.txt:md5,86a907217d64d4c2717885403058580f",
+                "multiqc_bcftools_stats.txt:md5,41a78d00bdca33cf0d2a558bb60838db",
+                "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
+                "multiqc_fastqc.txt:md5,ce26d17e62f3c8a1c9a01a871a4b9586",
+                "multiqc_general_stats.txt:md5,0814fb98fbb85e001e9c0c04d586d602",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,e97b7038c7155326b5d6a2289cc0aeb7",
+                "multiqc_whatshap_stats.txt:md5,5c4b972c8d52b3d997f117b39ba3ad5d",
+                "somalier_stats.txt:md5,fec840d4fe202c0e3ff7ce94b2a3bf92",
+                "whatshap-stats-table.txt:md5,d552daaaef1c92c3351ec2f4de64e6ad",
+                "FAM.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12",
+                "HG002_ONT_A_cramino_aligned_phased.arrow:md5,d2a5c81595fa34925ab8f03078487d81",
+                "HG002_ONT_B_cramino_aligned_phased.arrow:md5,61af72539e105cec79db7c9b78eb15a7",
+                "HG002_ONT_A_cramino_aligned.arrow:md5,d2a5c81595fa34925ab8f03078487d81",
+                "HG002_ONT_B_cramino_aligned.arrow:md5,61af72539e105cec79db7c9b78eb15a7",
+                "HG002_ONT_A.mosdepth.global.dist.txt:md5,5ae0972357f99aa481a0bf12fb9e0b0b",
+                "HG002_ONT_A.mosdepth.region.dist.txt:md5,023b1c6aeaf8fa5ededd6b711a5cd012",
+                "HG002_ONT_A.mosdepth.summary.txt:md5,c3b664b0983213f73edf3c0d5a0b04a2",
+                "HG002_ONT_A.regions.bed.gz:md5,da66d741bb69b5c259a8611848839dc7",
+                "HG002_ONT_A.regions.bed.gz.csi:md5,76f06311933695287c8716fe2c8a2d20",
+                "HG002_ONT_B.mosdepth.global.dist.txt:md5,e551c7a9d1a26cecc99d15ac93a4a924",
+                "HG002_ONT_B.mosdepth.region.dist.txt:md5,11154f617f447f4c59dc192d9af4249f",
+                "HG002_ONT_B.mosdepth.summary.txt:md5,bcb06b29c22cb6ad200f283e72c29653",
+                "HG002_ONT_B.regions.bed.gz:md5,1aa62d46a1e6683da3d44c59c502354b",
+                "HG002_ONT_B.regions.bed.gz.csi:md5,11db27a464f8996bae5521ee7d71c1ce",
+                "HG002_ONT_A_stats.blocks.tsv:md5,aac8023443ddf578ffcd11121391f1cf",
+                "HG002_ONT_A_stats.stats.tsv:md5,27fdac1e01e6491374c631239e6183aa",
+                "HG002_ONT_B_stats.blocks.tsv:md5,0adf84be03536262bf8d58eda524d709",
+                "HG002_ONT_B_stats.stats.tsv:md5,eb2a2c3b64feb8acff4df3a1b8d33b78",
+                "HG002_ONT_A_hificnv.copynum.bedgraph:md5,4c5517c1783afa11ff93c8d8627fbe42",
+                "HG002_ONT_A_hificnv.depth.bw:md5,69c333b205994200641ea539b4c277c6",
+                "HG002_ONT_A_hificnv.maf.bw:md5,5b46c27cc53cc8dd68903738ab220c5f",
+                "HG002_ONT_B_hificnv.copynum.bedgraph:md5,7d30f621d502d16301fa79cf48a3b903",
+                "HG002_ONT_B_hificnv.depth.bw:md5,5153fd5b008285e0fa0bcfe5026373bf",
+                "HG002_ONT_B_hificnv.maf.bw:md5,02eba7a84f1de8c042e071587a81d279"
+            ],
+            [
+                [
+                    "HG002_ONT_A_haplotagged.bam",
+                    "53495f0b494894437c243a5c5f47c4fc"
+                ],
+                [
+                    "HG002_ONT_B_haplotagged.bam",
+                    "325c284fc112dff72679b38c9ef2c2da"
+                ],
+                [
+                    "HG002_ONT_A.paraphase.bam",
+                    "7b8dc04d36dc2290fd031da73e8c8553"
+                ],
+                [
+                    "HG002_ONT_B.paraphase.bam",
+                    "7b8dc04d36dc2290fd031da73e8c8553"
+                ]
+            ],
+            [
+                [
+                    "HG002_ONT_A_hba.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=2101, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_B_hba.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=2101, phased=true, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_A_phased.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=236, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_B_phased.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=236, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snv_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=105, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_snvs_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=56, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_A_snvs_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=99, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_B_snvs_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=99, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=98, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "FAM_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz",
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=6, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_A_cnvs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=30, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_A_svs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=68, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_B_cnvs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=31, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "HG002_ONT_B_svs.vcf.gz",
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=68, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-22T15:35:40.786297675"
+    }
+}
\ No newline at end of file
diff --git a/workflows/nallo.nf b/workflows/nallo.nf
index ebf26251..28bf7506 100644
--- a/workflows/nallo.nf
+++ b/workflows/nallo.nf
@@ -1,5 +1,8 @@
-include { fromSamplesheet } from 'plugin/nf-validation'
-
+include { samplesheetToList } from 'plugin/nf-schema'
+include {
+    createReferenceChannelFromPath
+    createReferenceChannelFromSamplesheet
+} from '../subworkflows/local/utils_nfcore_nallo_pipeline'
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL SUBWORKFLOWS
@@ -7,23 +10,28 @@ include { fromSamplesheet } from 'plugin/nf-validation'
 */
 
 include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV     } from '../subworkflows/local/annotate_consequence_pli'
+include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SVS     } from '../subworkflows/local/annotate_consequence_pli'
+include { ANNOTATE_SVS                            } from '../subworkflows/local/annotate_svs'
 include { ANNOTATE_REPEAT_EXPANSIONS              } from '../subworkflows/local/annotate_repeat_expansions'
 include { ASSEMBLY                                } from '../subworkflows/local/genome_assembly'
 include { ASSEMBLY_VARIANT_CALLING                } from '../subworkflows/local/assembly_variant_calling'
 include { CONVERT_INPUT_FILES                     } from '../subworkflows/local/convert_input_files'
 include { BAM_INFER_SEX                           } from '../subworkflows/local/bam_infer_sex'
+include { CALL_CNVS                               } from '../subworkflows/local/call_cnvs'
 include { CALL_PARALOGS                           } from '../subworkflows/local/call_paralogs'
 include { CALL_REPEAT_EXPANSIONS                  } from '../subworkflows/local/call_repeat_expansions'
-include { CNV                                     } from '../subworkflows/local/cnv'
+include { CALL_SVS                                } from '../subworkflows/local/call_svs'
+include { FILTER_VARIANTS as FILTER_VARIANTS_SNVS } from '../subworkflows/local/filter_variants'
+include { FILTER_VARIANTS as FILTER_VARIANTS_SVS  } from '../subworkflows/local/filter_variants'
 include { METHYLATION                             } from '../subworkflows/local/methylation'
 include { PHASING                                 } from '../subworkflows/local/phasing'
 include { PREPARE_GENOME                          } from '../subworkflows/local/prepare_genome'
 include { QC_ALIGNED_READS                        } from '../subworkflows/local/qc_aligned_reads'
 include { RANK_VARIANTS as RANK_VARIANTS_SNV      } from '../subworkflows/local/rank_variants'
+include { RANK_VARIANTS as RANK_VARIANTS_SVS      } from '../subworkflows/local/rank_variants'
 include { SCATTER_GENOME                          } from '../subworkflows/local/scatter_genome'
 include { SHORT_VARIANT_CALLING                   } from '../subworkflows/local/short_variant_calling'
 include { SNV_ANNOTATION                          } from '../subworkflows/local/snv_annotation'
-include { STRUCTURAL_VARIANT_CALLING              } from '../subworkflows/local/structural_variant_calling'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -32,25 +40,26 @@ include { STRUCTURAL_VARIANT_CALLING              } from '../subworkflows/local/
 */
 
 // local
-include { CREATE_PEDIGREE_FILE as SAMPLESHEET_PED } from '../modules/local/create_pedigree_file'
-include { CREATE_PEDIGREE_FILE as SOMALIER_PED    } from '../modules/local/create_pedigree_file'
-include { ECHTVAR_ENCODE                          } from '../modules/local/echtvar/encode/main'
-include { FQCRS                                   } from '../modules/local/fqcrs'
-include { SAMTOOLS_MERGE                          } from '../modules/nf-core/samtools/merge/main'
+include { CREATE_PEDIGREE_FILE as SAMPLESHEET_PED           } from '../modules/local/create_pedigree_file/main'
+include { CREATE_PEDIGREE_FILE as SOMALIER_PED              } from '../modules/local/create_pedigree_file/main'
+include { CREATE_PEDIGREE_FILE as SOMALIER_PED_FAMILY       } from '../modules/local/create_pedigree_file/main'
+include { SAMTOOLS_MERGE                                    } from '../modules/nf-core/samtools/merge/main'
 
 // nf-core
-include { BCFTOOLS_CONCAT                         } from '../modules/nf-core/bcftools/concat/main'
-include { BCFTOOLS_PLUGINSPLIT                    } from '../modules/nf-core/bcftools/pluginsplit/main'
-include { BCFTOOLS_STATS                          } from '../modules/nf-core/bcftools/stats/main'
-include { CAT_FASTQ                               } from '../modules/nf-core/cat/fastq/main'
-include { FASTQC                                  } from '../modules/nf-core/fastqc/main'
-include { MINIMAP2_ALIGN                          } from '../modules/nf-core/minimap2/align/main'
-include { MULTIQC                                 } from '../modules/nf-core/multiqc/main'
-include { SPLITUBAM                               } from '../modules/nf-core/splitubam/main'
-include { paramsSummaryMap                        } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc                    } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML                  } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText                  } from '../subworkflows/local/utils_nfcore_nallo_pipeline'
+include { BCFTOOLS_CONCAT                                   } from '../modules/nf-core/bcftools/concat/main'
+include { BCFTOOLS_PLUGINSPLIT as BCFTOOLS_PLUGINSPLIT_SNVS } from '../modules/nf-core/bcftools/pluginsplit/main'
+include { BCFTOOLS_SORT                                     } from '../modules/nf-core/bcftools/sort/main'
+include { BCFTOOLS_STATS                                    } from '../modules/nf-core/bcftools/stats/main'
+include { MINIMAP2_ALIGN                                    } from '../modules/nf-core/minimap2/align/main'
+include { MULTIQC                                           } from '../modules/nf-core/multiqc/main'
+include { SPLITUBAM                                         } from '../modules/nf-core/splitubam/main'
+include { SVDB_MERGE as SVDB_MERGE_SVS_CNVS                 } from '../modules/nf-core/svdb/merge/main'
+include { TABIX_TABIX as TABIX_SVDB_MERGE_SVS_CNVS          } from '../modules/nf-core/tabix/tabix/main'
+include { paramsSummaryMap                                  } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc                              } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML                            } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText                            } from '../subworkflows/local/utils_nfcore_nallo_pipeline'
+include { citationBibliographyText                          } from '../subworkflows/local/utils_nfcore_nallo_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -64,148 +73,88 @@ workflow NALLO {
     ch_input
 
     main:
-    ch_vep_cache     = Channel.value([])
     ch_versions      = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-    // Optional input files that has to be set depending on which workflow is run
-    ch_cadd_header              = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect()
-    ch_cadd_resources           = params.cadd_resources             ? Channel.fromPath(params.cadd_resources).collect()
-                                                                    : ''
-    ch_cadd_prescored           = params.cadd_prescored             ? Channel.fromPath(params.cadd_prescored).collect()
-                                                                    : ''
-    ch_fasta                    = params.fasta                      ? Channel.fromPath(params.fasta).map { it -> [ it.simpleName, it ] }.collect()
-                                                                    : ''
-    ch_tandem_repeats           = params.tandem_repeats             ? Channel.fromPath(params.tandem_repeats).map{ [ it.simpleName, it ] }.collect()
-                                                                    : Channel.value([[],[]])
-    ch_input_bed                = params.bed                        ? Channel.fromPath(params.bed).map{ [ [ id:it.simpleName ] , it ] }.collect()
-                                                                    : Channel.value([[],[]])
-    ch_par                      = params.par_regions                ? Channel.fromPath(params.par_regions).map { [ [ id: it.simpleName ], it ] }.collect()
-                                                                    : ''
-    ch_trgt_bed                 = params.trgt_repeats               ? Channel.fromPath(params.trgt_repeats).map { it -> [ it.simpleName, it ] }.collect()
-                                                                    : ''
-    ch_variant_catalog          = params.variant_catalog            ? Channel.fromPath(params.variant_catalog).map { it -> [ it.simpleName, it ] }.collect()
-                                                                    : ''
-    ch_databases                = params.snp_db                     ? Channel.fromSamplesheet('snp_db', immutable_meta: false).map{ it[1] }.collect()
-                                                                    : ''
-    ch_variant_consequences_snv = params.variant_consequences_snv   ? Channel.fromPath(params.variant_consequences_snv).collect()
-                                                                    : Channel.value([])
-    ch_vep_cache_unprocessed    = params.vep_cache                  ? Channel.fromPath(params.vep_cache).map { it -> [ [ id:'vep_cache' ], it ] }.collect()
-                                                                    : Channel.value([[],[]])
-    ch_vep_extra_files_unsplit  = params.vep_plugin_files           ? Channel.fromPath(params.vep_plugin_files).collect()
-                                                                    : ''
-    ch_expected_xy_bed          = params.hificnv_xy                 ? Channel.fromPath(params.hificnv_xy).collect()
-                                                                    : ''
-    ch_expected_xx_bed          = params.hificnv_xx                 ? Channel.fromPath(params.hificnv_xx).collect()
-                                                                    : ''
-    ch_exclude_bed              = params.hificnv_exclude            ? Channel.fromPath(params.hificnv_exclude).collect()
-                                                                    : ''
-    ch_reduced_penetrance       = params.reduced_penetrance         ? Channel.fromPath(params.reduced_penetrance).collect()
-                                                                    : Channel.value([])
-    ch_score_config_snv         = params.score_config_snv           ? Channel.fromPath(params.score_config_snv).collect()
-                                                                    : Channel.value([])
-    ch_somalier_sites           = params.somalier_sites             ? Channel.fromPath(params.somalier_sites).map { [ it.simpleName, it ] }.collect()
-                                                                    : ''
-
-    // Check parameter that doesn't conform to schema validation here
-    if (params.phaser.matches('hiphase_sv|hiphase_snv') && params.preset == 'ONT_R10') { error "The HiPhase license only permits analysis of data from PacBio. For details see: https://github.com/PacificBiosciences/HiPhase/blob/main/LICENSE.md" }
-
-    // Read and store paths in the vep_plugin_files file
-    if (params.vep_plugin_files) {
-        ch_vep_extra_files_unsplit.splitCsv ( header:true )
-            .map { row ->
-                path = file(row.vep_files[0])
-                if(path.isFile() || path.isDirectory()){
-                    return [path]
-                } else {
-                    error("\nVep database file ${path} does not exist.")
-                }
-            }
-            .collect()
-            .set {ch_vep_extra_files}
-    }
+    // Channels from (optional) input files
+    // If provided: [[id: 'reference'], [/path/to/reference_full_name.file]]
+    ch_cadd_header               = createReferenceChannelFromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt")
+    ch_cadd_resources            = createReferenceChannelFromPath(params.cadd_resources)
+    ch_cadd_prescored_indels     = createReferenceChannelFromPath(params.cadd_prescored_indels)
+    ch_fasta                     = createReferenceChannelFromPath(params.fasta)
+    ch_tandem_repeats            = createReferenceChannelFromPath(params.tandem_repeats, Channel.value([[],[]]))
+    ch_input_bed                 = createReferenceChannelFromPath(params.target_regions, Channel.value([[],[]]))
+    ch_par                       = createReferenceChannelFromPath(params.par_regions)
+    ch_trgt_bed                  = createReferenceChannelFromPath(params.trgt_repeats)
+    ch_stranger_repeat_catalog   = createReferenceChannelFromPath(params.stranger_repeat_catalog)
+    ch_variant_consequences_snvs  = createReferenceChannelFromPath(params.variant_consequences_snvs)
+    ch_variant_consequences_svs  = createReferenceChannelFromPath(params.variant_consequences_svs)
+    ch_vep_cache_unprocessed     = createReferenceChannelFromPath(params.vep_cache, Channel.value([]))
+    ch_expected_xy_bed           = createReferenceChannelFromPath(params.hificnv_expected_xy_cn)
+    ch_expected_xx_bed           = createReferenceChannelFromPath(params.hificnv_expected_xx_cn)
+    ch_exclude_bed               = createReferenceChannelFromPath(params.hificnv_excluded_regions)
+    ch_genmod_reduced_penetrance = createReferenceChannelFromPath(params.genmod_reduced_penetrance)
+    ch_genmod_score_config_snvs  = createReferenceChannelFromPath(params.genmod_score_config_snvs)
+    ch_genmod_score_config_svs   = createReferenceChannelFromPath(params.genmod_score_config_svs)
+    ch_somalier_sites            = createReferenceChannelFromPath(params.somalier_sites)
+    ch_svdb_sv_databases         = createReferenceChannelFromPath(params.svdb_sv_databases)
+
+    // Channels from (optional) input samplesheets validated by schema
+    ch_databases                 = createReferenceChannelFromSamplesheet(params.echtvar_snv_databases, 'assets/schema_snp_db.json')
+    ch_vep_plugin_files          = createReferenceChannelFromSamplesheet(params.vep_plugin_files, 'assets/schema_vep_plugin_files.json', Channel.value([]))
+    ch_hgnc_ids                  = createReferenceChannelFromSamplesheet(params.filter_variants_hgnc_ids, 'assets/schema_hgnc_ids.json', Channel.value([]))
+        .map { it[0].toString() } // only one element per row
+        .collectFile(name: 'hgnc_ids.txt', newLine: true, sort: true)
+        .map { file -> [ [ id: 'hgnc_ids' ], file ] }
+        .collect()
 
     //
-    // Convert BAM files to FASTQ and vice versa
+    // Convert FASTQ to BAM (and vice versa if assembly workflow is active)
     //
-    CONVERT_INPUT_FILES ( ch_input )
+    CONVERT_INPUT_FILES (
+        ch_input,
+        !params.skip_genome_assembly, // should bam -> fastq conversion be done
+        !params.skip_alignment        // should fastq -> bam conversion be done
+    )
     ch_versions = ch_versions.mix(CONVERT_INPUT_FILES.out.versions)
 
     //
-    // Run raw (unaligned) read QC with FastQC and fqcrs
+    // Map reads to reference
     //
-    if(!params.skip_raw_read_qc) {
-
-        // Combine samples with multiple input files before QC - not ideal
-        CONVERT_INPUT_FILES.out.fastq
-            .groupTuple()
-            .branch { meta, reads ->
-                single: reads.size() == 1
-                    return [ meta, reads[0] ]
-                multiple: reads.size() > 1
-            }
-            .set { ch_fastq }
-
-        CAT_FASTQ ( ch_fastq.multiple )
-        ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
-
-        ch_fastq.single
-            .concat ( CAT_FASTQ.out.reads )
-            .set { raw_read_qc_in }
-
-        FASTQC ( raw_read_qc_in )
-        ch_versions = ch_versions.mix(FASTQC.out.versions)
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-
-        FQCRS ( raw_read_qc_in )
-        ch_versions = ch_versions.mix(FQCRS.out.versions)
-    }
-
-    //
-    // Prepare references
-    //
-    if(!params.skip_mapping_wf | !params.skip_assembly_wf ) {
+    if (!params.skip_alignment) {
 
+        // Prepeare references
         PREPARE_GENOME (
             ch_fasta,
             ch_vep_cache_unprocessed,
+            params.fasta.endsWith('.gz'),       // should we unzip fasta
+            params.vep_cache.endsWith("tar.gz") // should we untar vep cache
         )
         ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
-        if(!params.skip_snv_annotation) {
-            if (params.vep_cache) {
-                if (params.vep_cache.endsWith("tar.gz")) {
-                    ch_vep_cache = PREPARE_GENOME.out.vep_resources
-                } else {
-                    ch_vep_cache = Channel.fromPath(params.vep_cache).collect()
-                }
-            }
-        }
-
         // Gather indices
         fasta = PREPARE_GENOME.out.fasta
         fai   = PREPARE_GENOME.out.fai
         mmi   = PREPARE_GENOME.out.mmi
-    }
-
-    //
-    // (Split input files and), map reads to reference and merge into a single BAM per sample
-    //
-    if(!params.skip_mapping_wf) {
 
         // Split input files for alignment
-        if (params.parallel_alignments > 1) {
+        if (params.alignment_processes > 1) {
 
             SPLITUBAM ( CONVERT_INPUT_FILES.out.bam )
             ch_versions = ch_versions.mix(SPLITUBAM.out.versions)
-
-            reads_for_alignment = SPLITUBAM.out.bam.transpose()
-
-        } else {
-            reads_for_alignment = CONVERT_INPUT_FILES.out.bam
         }
-        // Align (split) reads
-        MINIMAP2_ALIGN ( reads_for_alignment, mmi, true, 'bai', false, false )
+
+        //
+        // Align reads (could be a split-align-merge subworkflow)
+        //
+        MINIMAP2_ALIGN (
+            params.alignment_processes > 1 ? SPLITUBAM.out.bam.transpose() : CONVERT_INPUT_FILES.out.bam,
+            mmi,
+            true,
+            'bai',
+            false,
+            false
+        )
         ch_versions = ch_versions.mix(MINIMAP2_ALIGN.out.versions)
 
         // Split channel into cases where we have multiple files or single files
@@ -224,12 +173,16 @@ workflow NALLO {
             .set { bam_to_merge }
 
         // Merge files if we have multiple files per sample
-        SAMTOOLS_MERGE ( bam_to_merge.multiple.map { meta, bam, bai -> [ meta, bam ] }, [[],[]], [[],[]], 'bai' )
+        SAMTOOLS_MERGE (
+            bam_to_merge.multiple.map { meta, bam, bai -> [ meta, bam ] },
+            [[],[]],
+            [[],[]]
+        )
         ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions)
 
         // Combine merged with unmerged bams
         SAMTOOLS_MERGE.out.bam
-            .join(SAMTOOLS_MERGE.out.index)
+            .join(SAMTOOLS_MERGE.out.bai)
             .concat(bam_to_merge.single)
             .map { meta, bam, bai -> [ meta - meta.subMap('n_files'), bam, bai ] }
             .set { bam_infer_sex_in }
@@ -238,7 +191,7 @@ workflow NALLO {
         // Create PED from samplesheet
         //
         ch_input
-            .map { meta, files -> [ meta.project, meta ] }
+            .map { meta, files -> [ [ id: meta.project ], meta ] }
             .groupTuple()
             .set { ch_samplesheet_ped_in }
 
@@ -246,258 +199,414 @@ workflow NALLO {
         ch_versions = ch_versions.mix(SAMPLESHEET_PED.out.versions)
 
         SAMPLESHEET_PED.out.ped
-            .map { project, ped -> [ [ 'id': project ], ped ] }
             .collect()
             .set { ch_samplesheet_pedfile }
 
         //
         // Check sex and relatedness, and update with infered sex if the sex for a sample is unknown
         //
-        BAM_INFER_SEX ( bam_infer_sex_in, fasta, fai, ch_somalier_sites, ch_samplesheet_pedfile )
+        BAM_INFER_SEX (
+            bam_infer_sex_in,
+            fasta,
+            fai,
+            ch_somalier_sites,
+            ch_samplesheet_pedfile
+        )
         ch_versions = ch_versions.mix(BAM_INFER_SEX.out.versions)
-
         ch_multiqc_files = ch_multiqc_files.mix(BAM_INFER_SEX.out.somalier_samples.map{it[1]}.collect().ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(BAM_INFER_SEX.out.somalier_pairs.map{it[1]}.collect().ifEmpty([]))
 
+        // Set files with updated meta for subsequent processes
         bam     = BAM_INFER_SEX.out.bam
         bai     = BAM_INFER_SEX.out.bai
         bam_bai = BAM_INFER_SEX.out.bam_bai
 
-        //
-        // Create PED with updated sex
-        //
-        bam
-            .map { meta, files -> [ meta.project, meta ] }
-            .groupTuple()
-            .set { ch_somalier_ped_in }
+    }
 
-        SOMALIER_PED ( ch_somalier_ped_in )
-        ch_versions = ch_versions.mix(SOMALIER_PED.out.versions)
+    //
+    // Run read QC with FastQC, mosdepth and cramino
+    //
+    if (!params.skip_qc) {
 
-        SOMALIER_PED.out.ped
-            .map { project, ped -> [ [ 'id': project ], ped ] }
-            .collect()
-            .set { ch_updated_pedfile }
+        QC_ALIGNED_READS (
+            bam_bai,
+            fasta,
+            ch_input_bed
+        )
+        ch_versions = ch_versions.mix(QC_ALIGNED_READS.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.fastqc_zip.collect { it[1] }.ifEmpty([]) )
+        ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_summary.collect { it[1] } )
+        ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_global_dist.collect { it[1] } )
+        ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_region_dist.collect { it[1] }.ifEmpty([]) )
 
-        //
-        // Run aligned read QC with mosdepth and cramino
-        //
-        if (!params.skip_aligned_read_qc) {
-            QC_ALIGNED_READS( bam_bai, fasta, ch_input_bed )
-            ch_versions = ch_versions.mix(QC_ALIGNED_READS.out.versions)
+    }
 
-            ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_summary.collect { it[1] } )
-            ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_global_dist.collect { it[1] } )
-            ch_multiqc_files = ch_multiqc_files.mix( QC_ALIGNED_READS.out.mosdepth_region_dist.collect { it[1] }.ifEmpty([]) )
-        }
+    //
+    // Call paralogous genes with paraphase
+    //
+    if(!params.skip_call_paralogs) {
+        CALL_PARALOGS (
+            bam_bai,
+            fasta
+        )
+        ch_versions = ch_versions.mix(CALL_PARALOGS.out.versions)
+    }
 
-        //
-        // Call paralogous genes with paraphase
-        //
-        if(!params.skip_call_paralogs) {
-            CALL_PARALOGS ( bam_bai, fasta )
-            ch_versions = ch_versions.mix(CALL_PARALOGS.out.versions)
-        }
+    //
+    // Hifiasm assembly and assembly variant calling
+    //
+    if(!params.skip_genome_assembly) {
+
+        //Hifiasm assembly
+        ASSEMBLY( CONVERT_INPUT_FILES.out.fastq )
+        ch_versions = ch_versions.mix(ASSEMBLY.out.versions)
+
+        // Update assembly variant calling meta with sex from somalier
+        ASSEMBLY.out.assembled_haplotypes
+            .map { meta, hap1, hap2 -> [ meta.id, [ hap1, hap2 ] ] }
+            .set { haplotypes }
+
+        bam
+            .map { meta, bam -> [ meta.id, meta ] }
+            .join( haplotypes )
+            .map { id, meta, haplotypes -> [ meta, haplotypes[0], haplotypes[1] ] }
+            .set { ch_assembly_variant_calling_in }
+
+        // Run dipcall
+        ASSEMBLY_VARIANT_CALLING (
+            ch_assembly_variant_calling_in,
+            fasta,
+            fai,
+            ch_par
+        )
+        ch_versions = ch_versions.mix(ASSEMBLY_VARIANT_CALLING.out.versions)
+    }
+
+    //
+    // Call SNVs
+    //
+    if(!params.skip_snv_calling) {
 
         //
-        // Hifiasm assembly and assembly variant calling
+        // Make BED intervals, to be used for parallel SNV calling
         //
-        if(!params.skip_assembly_wf) {
+        SCATTER_GENOME (
+            fai,
+            ch_input_bed,             // BED file to scatter
+            !params.target_regions,   // Make bed from fai
+            !params.skip_snv_calling,
+            params.snv_calling_processes
+        )
+        ch_versions = ch_versions.mix(SCATTER_GENOME.out.versions)
+
+        // Combine to create a bam_bai - interval pair for each sample
+        bam_bai
+            .combine( SCATTER_GENOME.out.bed_intervals )
+            .map { meta, bam, bai, bed, intervals ->
+                [ meta + [ num_intervals: intervals ], bam, bai, bed ]
+            }
+            .set{ ch_snv_calling_in }
+
+        // This subworkflow calls SNVs with DeepVariant and outputs:
+        // 1. A merged and normalised VCF, containing one sample with all regions, to be used in downstream subworkflows requiring SNVs.
+        // 2. A merged and normalised VCF, containing one region with all samples, to be used in annotation and ranking.
+        SHORT_VARIANT_CALLING( ch_snv_calling_in, fasta, fai, SCATTER_GENOME.out.bed, ch_par )
+        ch_versions = ch_versions.mix(SHORT_VARIANT_CALLING.out.versions)
 
-            //Hifiasm assembly
-            ASSEMBLY( CONVERT_INPUT_FILES.out.fastq )
-            ch_versions = ch_versions.mix(ASSEMBLY.out.versions)
+        SHORT_VARIANT_CALLING.out.family_bcf
+            .join( SHORT_VARIANT_CALLING.out.family_csi )
+            .set { ch_vcf_tbi_per_region }
+    }
+
+    //
+    // Annotate SNVs
+    //
+    if(!params.skip_snv_annotation) {
+
+        // Annotates family VCFs per variant call region
+        SNV_ANNOTATION(
+            SHORT_VARIANT_CALLING.out.family_bcf,
+            ch_databases.map { meta, databases -> databases }.collect(),
+            fasta,
+            fai.map { name, fai -> [ [ id: name ], fai ] },
+            PREPARE_GENOME.out.vep_resources.map { meta, cache -> cache },
+            params.vep_cache_version,
+            ch_vep_plugin_files.collect(),
+            (params.cadd_resources && params.cadd_prescored_indels), // should indels be annotated with CADD
+            ch_cadd_header,
+            ch_cadd_resources,
+            ch_cadd_prescored_indels
+        )
+        ch_versions = ch_versions.mix(SNV_ANNOTATION.out.versions)
 
-            // Update assembly variant calling meta with sex from somalier
-            ASSEMBLY.out.assembled_haplotypes
-                .map { meta, hap1, hap2 -> [ meta.id, [ hap1, hap2 ] ] }
-                .set { haplotypes }
+        ANN_CSQ_PLI_SNV (
+            SNV_ANNOTATION.out.vcf,
+            ch_variant_consequences_snvs
+        )
+        ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)
+
+        ANN_CSQ_PLI_SNV.out.vcf
+            .join( ANN_CSQ_PLI_SNV.out.tbi )
+            .set { ch_vcf_tbi_per_region }
+
+    }
+
+    //
+    // Ranks family VCFs per variant call region
+    // Can only run if samplesheet has affected samples
+    //
+    if(!params.skip_rank_variants) {
 
+        // Create PED with updated sex - per family
+        SOMALIER_PED_FAMILY (
             bam
-                .map { meta, bam -> [ meta.id, meta ] }
-                .join( haplotypes )
-                .map { id, meta, haplotypes -> [ meta, haplotypes[0], haplotypes[1] ] }
-                .set { ch_assembly_variant_calling_in }
-
-            // Run dipcall
-            ASSEMBLY_VARIANT_CALLING( ch_assembly_variant_calling_in, fasta, fai , ch_par)
-            ch_versions = ch_versions.mix(ASSEMBLY_VARIANT_CALLING.out.versions)
-        }
+                .map { meta, files -> [ [ id: meta.family_id ], meta ] }
+                .groupTuple()
+        )
+        ch_versions = ch_versions.mix(SOMALIER_PED_FAMILY.out.versions)
+
+        // Give PED file SNV meta so they can be joined later in the subworkflow.
+        // Since we don't always have matching number of ped files and call regions
+        // we need to combine and filter instead of join
+        ANN_CSQ_PLI_SNV.out.vcf
+            .map { meta, vcf -> [ [ id:meta.family_id ], meta ] }
+            .combine ( SOMALIER_PED_FAMILY.out.ped )
+            .filter { family_id_snv, meta, family_id_ped, ped -> family_id_snv == family_id_ped }
+            .map { family_id_snv, meta, family_id_ped, ped -> [ meta, ped ] }
+            .set { snv_ranking_ped_file }
+
+        // Only run if we have affected individuals
+        RANK_VARIANTS_SNV (
+            ANN_CSQ_PLI_SNV.out.vcf,
+            snv_ranking_ped_file,
+            ch_genmod_reduced_penetrance,
+            ch_genmod_score_config_snvs
+        )
+        ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions)
 
-        //
-        // Call SVs with Sniffles2
-        STRUCTURAL_VARIANT_CALLING( bam_bai, fasta, fai, ch_tandem_repeats )
-        ch_versions = ch_versions.mix(STRUCTURAL_VARIANT_CALLING.out.versions)
+        RANK_VARIANTS_SNV.out.vcf
+            .join( RANK_VARIANTS_SNV.out.tbi )
+            .set { ch_vcf_tbi_per_region }
+    }
+
+    //
+    // Concatenate, sort, split, make database and get statistics of SNVs (should be a subworkflow)
+    //
+    if(!params.skip_snv_calling) {
+
+        ch_vcf_tbi_per_region
+            .map { meta, vcf, tbi -> [ [ id: meta.family_id ], vcf, tbi ] }
+            .groupTuple()
+            .set { ch_bcftools_concat_in }
+
+        // Concat into family VCFs per family with all regions
+        BCFTOOLS_CONCAT (
+                ch_bcftools_concat_in
+            )
+        ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions)
+
+        // Sort and publish
+        BCFTOOLS_SORT ( BCFTOOLS_CONCAT.out.vcf )
+        ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions)
+
+        // Split family VCFs to also publish a VCF per sample
+        BCFTOOLS_PLUGINSPLIT_SNVS ( BCFTOOLS_SORT.out.vcf.join(BCFTOOLS_SORT.out.tbi ), [], [], [], [] )
+        ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT_SNVS.out.versions)
+
+        BCFTOOLS_PLUGINSPLIT_SNVS.out.vcf
+            .transpose()
+            .map { meta, vcf -> [ meta, vcf, [] ] }
+            .set { ch_bcftools_stats_snv_in }
+
+        BCFTOOLS_STATS ( ch_bcftools_stats_snv_in, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]] )
+        ch_versions = ch_versions.mix(BCFTOOLS_STATS.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_STATS.out.stats.collect{it[1]}.ifEmpty([]))
+
+    }
+    //
+    // Filter SNVs
+    //
+    if(params.filter_variants_hgnc_ids || params.filter_snvs_expression != '') {
+
+        // Publish filtered `project` SNVs from here
+        FILTER_VARIANTS_SNVS (
+            BCFTOOLS_SORT.out.vcf,
+            ch_hgnc_ids,
+            params.filter_variants_hgnc_ids
+        )
+        ch_versions = ch_versions.mix(FILTER_VARIANTS_SNVS.out.versions)
+
+    }
+
+    //
+    // Call SVs
+    //
+    if(!params.skip_alignment) {
+
+        // If both CNV-calling and SV annotation is off, merged variants are output from here
+        CALL_SVS (
+            bam_bai,
+            fasta,
+            fai,
+            params.sv_caller,
+            ch_tandem_repeats,
+            ch_input_bed
+        )
+        ch_versions = ch_versions.mix(CALL_SVS.out.versions)
+
+        CALL_SVS.out.family_vcf
+            .set { annotate_svs_in }
+    }
+
+    //
+    // Call CNVs with HiFiCNV
+    //
+    if(!params.skip_cnv_calling) {
+
+        CALL_CNVS (
+            bam_bai.join(SHORT_VARIANT_CALLING.out.snp_calls_vcf),
+            fasta,
+            ch_expected_xy_bed,
+            ch_expected_xx_bed,
+            ch_exclude_bed
+        )
+        ch_versions = ch_versions.mix(CALL_CNVS.out.versions)
+
+    }
+
+    //
+    // Merge SVs and CNVs if we've called both SVs and CNVs
+    //
+    if (!params.skip_cnv_calling) {
+
+        CALL_SVS.out.family_vcf
+            .join(CALL_CNVS.out.family_vcf)
+            .map { meta, svs, cnvs -> [ meta, [ svs, cnvs ] ] }
+            .set { svdb_merge_svs_cnvs_in }
+
+        // If SV annotation is off, merged variants are output from here (should be a merge and index subworkflow)
+        SVDB_MERGE_SVS_CNVS (
+            svdb_merge_svs_cnvs_in,
+            ['svs', 'cnvs'], // Because SVs have better breakpoint resolution, give them priority
+            true
+        )
+        ch_versions = ch_versions.mix(SVDB_MERGE_SVS_CNVS.out.versions)
+
+        SVDB_MERGE_SVS_CNVS.out.vcf
+            .set { annotate_svs_in }
+    }
+
+    //
+    // Index the merged SVs and SVs if not skipping sv annotation (should be a merge and index subworkflow)
+    //
+    if (!params.skip_sv_annotation) {
+
+        TABIX_SVDB_MERGE_SVS_CNVS ( SVDB_MERGE_SVS_CNVS.out.vcf )
+        ch_versions = ch_versions.mix(TABIX_SVDB_MERGE_SVS_CNVS.out.versions)
+    }
+
+    //
+    // Annotate SVs
+    //
+    if (!params.skip_sv_annotation) {
+
+        // If annotation is on, then merged variants are output from here
+        ANNOTATE_SVS (
+            annotate_svs_in,
+            fasta,
+            ch_svdb_sv_databases,
+            PREPARE_GENOME.out.vep_resources.map { meta, cache -> cache },
+            params.vep_cache_version,
+            ch_vep_plugin_files.collect()
+        )
+        ch_versions = ch_versions.mix(ANNOTATE_SVS.out.versions)
+
+        ANN_CSQ_PLI_SVS (
+            ANNOTATE_SVS.out.vcf,
+            ch_variant_consequences_svs
+        )
+        ch_versions = ch_versions.mix(ANN_CSQ_PLI_SVS.out.versions)
+    }
+
+    //
+    // Rank SVs
+    //
+    if (!params.skip_rank_variants) {
+
+        RANK_VARIANTS_SVS (
+            ANN_CSQ_PLI_SVS.out.vcf,
+            SOMALIER_PED_FAMILY.out.ped,
+            ch_genmod_reduced_penetrance,
+            ch_genmod_score_config_svs
+        )
+        ch_versions = ch_versions.mix(RANK_VARIANTS_SVS.out.versions)
+    }
 
         //
-        // Call (and annotate and rank) SNVs
+        // Filter SVs
         //
-        if(!params.skip_short_variant_calling) {
-
-            //
-            // Make BED intervals, to be used for parallel SNV calling
-            //
-            SCATTER_GENOME (
-                fai,
-                ch_input_bed,
-                !params.bed,
-                !params.skip_short_variant_calling,
-                params.parallel_snv
-            )
-            ch_versions = ch_versions.mix(SCATTER_GENOME.out.versions)
-
-            // Combine to create a bam_bai - interval pair for each sample
-            bam_bai
-                .combine( SCATTER_GENOME.out.bed_intervals )
-                .map { meta, bam, bai, bed, intervals ->
-                    [ meta + [ num_intervals: intervals ], bam, bai, bed ]
-                }
-                .set{ ch_snv_calling_in }
-
-            //
-            // This subworkflow calls SNVs with DeepVariant and outputs:
-            // 1. A merged and normalised VCF, containing one sample with all regions, to be used in downstream subworkflows requiring SNVs.
-            // 2. A merged and normalised VCF, containing one region with all samples, to be used in annotation and ranking.
-            //
-            SHORT_VARIANT_CALLING( ch_snv_calling_in, fasta, fai, SCATTER_GENOME.out.bed, ch_par )
-            ch_versions = ch_versions.mix(SHORT_VARIANT_CALLING.out.versions)
-
-            //
-            // Annotate SNVs
-            //
-            if(!params.skip_snv_annotation) {
-
-                //
-                // Annotates one multisample VCF per variant call region
-                //
-                SNV_ANNOTATION(
-                    SHORT_VARIANT_CALLING.out.combined_bcf,
-                    ch_databases,
-                    fasta,
-                    fai.map { name, fai -> [ [ id: name ], fai ] },
-                    ch_vep_cache,
-                    params.vep_cache_version,
-                    ch_vep_extra_files,
-                    (params.cadd_resources && params.cadd_prescored),
-                    ch_cadd_header,
-                    ch_cadd_resources,
-                    ch_cadd_prescored
-                )
-                ch_versions = ch_versions.mix(SNV_ANNOTATION.out.versions)
-
-                ANN_CSQ_PLI_SNV (
-                    SNV_ANNOTATION.out.vcf,
-                    ch_variant_consequences_snv
-                )
-                ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)
-
-                //
-                // Ranks one multisample VCF per variant call region
-                //
-                if(!params.skip_rank_variants) {
-                    // Only run if we have affected individuals
-                    RANK_VARIANTS_SNV (
-                        ANN_CSQ_PLI_SNV.out.vcf_ann.filter { meta, vcf -> meta.contains_affected },
-                        ch_updated_pedfile.map { meta, ped -> ped },
-                        ch_reduced_penetrance,
-                        ch_score_config_snv
-                    )
-                    ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions)
-
-                    // If there are affected individuals and RANK_VARIANTS has been run,
-                    // input that to VCF concatenation
-                    RANK_VARIANTS_SNV.out.vcf
-                        .join( RANK_VARIANTS_SNV.out.tbi )
-                        .set { ch_vcf_tbi_per_region }
-                } else {
-                    // otherwise grab the VCF that should have gone into RANK_VARIANTS
-                    ANN_CSQ_PLI_SNV.out.vcf_ann
-                        .join( ANN_CSQ_PLI_SNV.out.tbi_ann )
-                        .set { ch_vcf_tbi_per_region }
-                }
-            } else {
-                // If neither snv_annotation nor rank_variants was run, take the output from
-                // SHORT_VARIANT_CALLING
-                SHORT_VARIANT_CALLING.out.combined_bcf
-                    .join( SHORT_VARIANT_CALLING.out.combined_csi )
-                    .set { ch_vcf_tbi_per_region }
-            }
+        if(params.filter_variants_hgnc_ids || params.filter_svs_expression != '') {
 
-            ch_vcf_tbi_per_region
-                .map { meta, vcf, tbi -> [ [ id: meta.project ], vcf, tbi ] }
-                .groupTuple()
-                .set { ch_bcftools_concat_in }
-
-            // Concat into a multisample VCF with all regions and publish
-            BCFTOOLS_CONCAT ( ch_bcftools_concat_in )
-            ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions)
-
-            // Make an echtvar database of all samples
-            ECHTVAR_ENCODE ( BCFTOOLS_CONCAT.out.vcf )
-            ch_versions = ch_versions.mix(ECHTVAR_ENCODE.out.versions)
-
-            // Split multisample VCF to also publish a VCF per sample
-            BCFTOOLS_PLUGINSPLIT ( BCFTOOLS_CONCAT.out.vcf.join(BCFTOOLS_CONCAT.out.tbi ), [], [], [], [] )
-            ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT.out.versions)
-
-            BCFTOOLS_PLUGINSPLIT.out.vcf
-                .transpose()
-                .map { meta, vcf -> [ meta, vcf, [] ] }
-                .set { ch_bcftools_stats_snv_in }
-
-            BCFTOOLS_STATS ( ch_bcftools_stats_snv_in, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]] )
-            ch_versions = ch_versions.mix(BCFTOOLS_STATS.out.versions)
-            ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_STATS.out.stats.collect{it[1]}.ifEmpty([]))
-
-            //
-            // Call CNVs with HiFiCNV
-            //
-            if(!params.skip_cnv_calling) {
-                bam_bai
-                    .join(SHORT_VARIANT_CALLING.out.snp_calls_vcf)
-                    .set { cnv_workflow_in }
-
-                CNV(cnv_workflow_in, fasta, ch_expected_xy_bed, ch_expected_xx_bed, ch_exclude_bed)
-                ch_versions = ch_versions.mix(CNV.out.versions)
+            if(params.skip_cnv_calling) {
+                ch_filter_svs_in = params.skip_sv_annotation ? CALL_SVS.out.family_vcf : params.skip_rank_variants ? ANN_CSQ_PLI_SVS.out.vcf : RANK_VARIANTS_SVS.out.vcf
+            } else {
+                ch_filter_svs_in = params.skip_sv_annotation ? annotate_svs_in : params.skip_rank_variants ? ANN_CSQ_PLI_SVS.out.vcf : RANK_VARIANTS_SVS.out.vcf
             }
 
-            //
-            // Phase SNVs and INDELs
-            //
-            if(!params.skip_phasing_wf) {
-
-                PHASING( SHORT_VARIANT_CALLING.out.snp_calls_vcf, STRUCTURAL_VARIANT_CALLING.out.ch_sv_calls_vcf, bam_bai, fasta, fai)
-                ch_versions = ch_versions.mix(PHASING.out.versions)
-
-                ch_multiqc_files = ch_multiqc_files.mix(PHASING.out.stats.collect{it[1]}.ifEmpty([]))
-
-                //
-                // Create methylation pileups with modkit
-                //
-                if(!params.skip_methylation_wf) {
-
-                    METHYLATION( PHASING.out.haplotagged_bam_bai, fasta, fai, ch_input_bed )
-                    ch_versions = ch_versions.mix(METHYLATION.out.versions)
-                }
-
-                //
-                // Call repeat expansions with TRGT
-                //
-                if(!params.skip_repeat_calling) {
-
-                    CALL_REPEAT_EXPANSIONS ( PHASING.out.haplotagged_bam_bai, fasta, fai, ch_trgt_bed )
-                    ch_versions = ch_versions.mix(CALL_REPEAT_EXPANSIONS.out.versions)
-
-                    //
-                    // Annotate repeat expansions with stranger
-                    //
-                    if(!params.skip_repeat_annotation) {
-                        ANNOTATE_REPEAT_EXPANSIONS ( ch_variant_catalog, CALL_REPEAT_EXPANSIONS.out.vcf )
-                        ch_versions = ch_versions.mix(ANNOTATE_REPEAT_EXPANSIONS.out.versions)
-                    }
-                }
-            }
+            FILTER_VARIANTS_SVS (
+                ch_filter_svs_in,
+                ch_hgnc_ids,
+                params.filter_variants_hgnc_ids
+            )
         }
+
+    //
+    // Phase SNVs and INDELs
+    //
+    if(!params.skip_phasing) {
+
+        PHASING (
+            SHORT_VARIANT_CALLING.out.snp_calls_vcf,
+            SHORT_VARIANT_CALLING.out.snp_calls_tbi,
+            bam_bai,
+            fasta,
+            fai
+        )
+        ch_versions = ch_versions.mix(PHASING.out.versions)
+
+        ch_multiqc_files = ch_multiqc_files.mix(PHASING.out.stats.collect{it[1]}.ifEmpty([]))
+
+    }
+
+    //
+    // Create methylation pileups with modkit
+    //
+    if(!params.skip_methylation_pileups) {
+        METHYLATION (
+            !params.skip_phasing ? PHASING.out.haplotagged_bam_bai : bam_bai,
+            fasta,
+            fai,
+            ch_input_bed,
+        )
+        ch_versions = ch_versions.mix(METHYLATION.out.versions)
+    }
+
+    //
+    // Call repeat expansions with TRGT
+    //
+    if(!params.skip_repeat_calling) {
+
+        CALL_REPEAT_EXPANSIONS ( PHASING.out.haplotagged_bam_bai, fasta, fai, ch_trgt_bed )
+        ch_versions = ch_versions.mix(CALL_REPEAT_EXPANSIONS.out.versions)
+    }
+
+    //
+    // Annotate repeat expansions with stranger
+    //
+    if(!params.skip_repeat_annotation) {
+
+        ANNOTATE_REPEAT_EXPANSIONS ( ch_stranger_repeat_catalog, CALL_REPEAT_EXPANSIONS.out.family_vcf )
+        ch_versions = ch_versions.mix(ANNOTATE_REPEAT_EXPANSIONS.out.versions)
     }
 
     //
@@ -506,7 +615,7 @@ workflow NALLO {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name:  'nallo_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
@@ -526,28 +635,44 @@ workflow NALLO {
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
 
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
-        methodsDescriptionText(ch_multiqc_custom_methods_description))
-
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_methods_description                = Channel.of(
+        methodsDescriptionText(ch_multiqc_custom_methods_description)
+    )
+    ch_methods_description_citation       = citationBibliographyText(
+        ch_versions,
+        file("$projectDir/assets/software_references.yml"),
+        'citation'
+    )
+    ch_methods_description_bibliography   = citationBibliographyText(
+        ch_versions,
+        file("$projectDir/assets/software_references.yml"),
+        'bibliography'
+    )
     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: true
-        )
+        ch_methods_description
+            .concat(ch_methods_description_citation)
+            .concat(ch_methods_description_bibliography)
+            .flatten()
+            .collectFile(
+                name: 'methods_description_mqc.yaml',
+                sort: false // preserve order for correct yaml structure
+            )
     )
 
     MULTIQC (
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 
     emit: