diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 0000000..a425e09
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,80 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+    default: ""
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-java@0f481fcb613427c0f801b606911222b5b6f3083a # v5
+      with:
+        distribution: "temurin"
+        java-version: "17"
+
+    - name: Set up nf-test
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
+      with:
+        version: ${{ env.NFT_VER }}
+        install-fast-diff: true
+
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Prepare tag parameter if tags are provided
+        TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
+
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --dry-run \
+          --profile singularity \
+          ${TAGS} \
+          --filter process,workflow \
+          ${{ inputs.paths }}) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
new file mode 100644
index 0000000..54c17c0
--- /dev/null
+++ b/.github/actions/nf-test-action/action.yml
@@ -0,0 +1,110 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps (singularity only)"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+  tags:
+    description: "Tag to pass as argument for nf-test --tag parameter"
+    required: false
+    default: ""
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-java@0f481fcb613427c0f801b606911222b5b6f3083a # v5
+      with:
+        distribution: "temurin"
+        java-version: "17"
+
+    - name: Set up Nextflow
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      with:
+        version: "${{ env.NXF_VER }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
+      with:
+        python-version: "3.14"
+
+    - name: Set up nf-test
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
+      with:
+        version: "${{ env.NFT_VER }}"
+        install-fast-diff: true
+
+    - name: Set up apptainer
+      shell: bash
+      run: |
+        sudo apt update
+        sudo apt install -y software-properties-common
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt update
+        sudo apt install -y apptainer apptainer-suid
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Run nf-test
+      id: run-nf-test
+      shell: bash
+      run: |
+        TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
+
+        nf-test test \
+          --profile=${{ inputs.profile }} \
+          --tap=test.tap \
+          --verbose \
+          --ci \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
+          --filter process,workflow \
+          $TAGS \
+          ${{ inputs.paths }}
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: ${{ failure() && steps.run-nf-test.conclusion == 'failure' }}
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test Results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..15e748e
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,174 @@
+name: Run Linting
+on:
+  pull_request:
+    branches: [main, develop, release/*, feature/*]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NXF_VER: "25.10.2"
+  NXF_SYNTAX_PARSER: "v2"
+
+jobs:
+  ###################
+  # nf-core linting #
+  ###################
+  nf-core-changes:
+    name: nf-core-changes
+    runs-on: ubuntu-latest
+
+    outputs:
+      # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files
+      modules: ${{ steps.filter.outputs.modules }}
+      modules_files: ${{ steps.module_names.outputs.result }}
+      subworkflows: ${{ steps.filter.outputs.subworkflows }}
+      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
+
+      - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
+        id: filter
+        with:
+          filters: |
+            modules:
+              - added|modified: 'modules/UMCUGenetics/**'
+            subworkflows:
+              - added|modified: 'subworkflows/UMCUGenetics/**'
+          token: ""
+          list-files: "json"
+
+      - name: Get module name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.modules_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('modules/UMCUGenetics/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+      - name: Get subworkflow name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: subworkflow_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('subworkflows/UMCUGenetics/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+
+      - name: debug
+        run: |
+          echo ${{ steps.filter.outputs.modules_files }}
+          echo ${{ steps.module_names.outputs.result }}
+          echo ${{ steps.filter.outputs.subworkflows_files }}
+          echo ${{ steps.subworkflow_names.outputs.result }}
+
+  nf-core-lint-modules:
+    runs-on: ubuntu-latest
+    name: nf-core lint modules
+    needs: nf-core-changes
+    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
+        id: cache-pip
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: |
+            ${{ runner.os }}-pip
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/UMCUGenetics/nf-core-tools.git
+
+      - name: Lint module ${{ matrix.module }}
+        run: nf-core modules lint ${{ matrix.module }}
+
+  nf-core-lint-subworkflows:
+    runs-on: ubuntu-latest
+    name: nf-core lint subworkflows
+    needs: nf-core-changes
+    if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/UMCUGenetics/nf-core-tools.git
+
+      - name: Lint subworkflow ${{ matrix.subworkflow }}
+        run: nf-core subworkflows lint ${{ matrix.subworkflow }}
+
+  confirm-pass-lint:
+    runs-on: ubuntu-latest
+    needs: [nf-core-lint-modules, nf-core-lint-subworkflows]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 0000000..dc5fb93
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,116 @@
+name: Run nf-test
+on:
+  pull_request:
+    branches: [main, develop, release/*, feature/*]
+    paths-ignore:
+      - "**/meta.yml"
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFT_VER: "0.9.5"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VER: "25.10.2"
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose detected component paths and shard info
+      paths: ${{ steps.list.outputs.components }}
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6
+        with:
+          head: ${{ github.sha }}
+          base: ${{ github.event.pull_request.base.sha || 'origin/main' }}
+          n_parents: 0
+          exclude_tags: "gpu"
+
+      - name: get number of shards
+        id: set-shards
+        if: ${{ steps.list.outputs.components != '[]' }}
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 16
+          paths: "${{ join(fromJson(steps.list.outputs.components ), ' ') }}"
+
+      - name: debug
+        run: |
+          echo ${{ steps.list.outputs.components }}
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    runs-on: ubuntu-latest
+    name: "singularity | ${{ matrix.shard }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [singularity]
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+    outputs:
+      paths: ${{ needs.nf-test-changes.outputs.paths }}
+
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test Action
+        if: ${{ needs.nf-test-changes.outputs.paths != '[]' }}
+        uses: ./.github/actions/nf-test-action
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+          paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}"
+
+  confirm-pass-nf-test:
+    runs-on: ubuntu-latest
+    needs: [nf-test]
+    if: always()
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
diff --git a/.nf-core.yml b/.nf-core.yml
new file mode 100644
index 0000000..406f531
--- /dev/null
+++ b/.nf-core.yml
@@ -0,0 +1,10 @@
+org_path: UMCUGenetics
+repository_type: modules
+lint:
+  main_nf:
+    - when_exist
+    - test_main_tags
+    - container_links
+  module_tests:
+    - test_main_tags
+  meta_yml: false
diff --git a/README.md b/README.md
index 016d434..c69f2b8 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,55 @@
-# Modules
\ No newline at end of file
+# Modules
+
+
+## Repository Structure
+
+``` sh
+.
+├── README.md
+├── main.nf
+└── modules
+    └── UMCUGenetics
+```
+
+Modules are placed under the `./modules/UMCUGenetics/` folder in the format tool/subtool. For example `./modules/UMCUGenetics/samtools/view/`
+
+
+## Linting configuration
+Note: A fork of the nf-core CLI tools is used to run the linting actions (https://github.com/UMCUGenetics/nf-core-tools.git). This was done to make the linting of modules more customisable. For our purposes not all requirements by nf-core are neccesary.
+Linting configuration of this repository is configured in `.nf-core.yml` and is structured similarly to how `nf-core pipeline lint` configuration works (note that the tests in the yaml file are the ones being skipped, all the others are enabled). Usually, it is not neccessary to change this, but to view all available modules linting options:
+
+``` sh
+nf-core modules lint --list
+```
+
+Install the forked nf-core tools locally:
+
+``` sh
+pip install git+https://github.com/UMCUGenetics/nf-core-tools.git
+```
+
+### Github actions
+Linting is triggered automatically upon creating a pull request through a github actions workflow [.github/workflows/lint.yml]. The actions workflow is adapted from the actions workflow used in the [nf-core/modules](https://github.com/nf-core/modules) repository, with mostly small changes that remove nf-core specific action runners.
+
+### Running linting
+
+Alternatively, linting test can be manually executed:
+
+``` sh
+cd ./modules
+nf-core modules lint <tool/command>
+# Example: nf-core modules lint pgscatalog/combine
+```
+
+
+
+## Testing configuration
+TODO
+
+
+## Using a module in a nextflow pipeline
+Modules in this repository can be added to a pipeline similarly to how nf-core modules are installed.
+
+``` sh
+nf-core modules --git-remote https://github.com/UMCUGenetics/Modules install pgscatalog/combine
+```
diff --git a/main.nf b/main.nf
new file mode 100644
index 0000000..de12f61
--- /dev/null
+++ b/main.nf
@@ -0,0 +1,3 @@
+/*
+ * not actually used - just a placeholder
+ */
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 0000000..609c4c9
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,14 @@
+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 = "tests/config/nf-test.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile = ""
+
+}
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
new file mode 100644
index 0000000..24bd660
--- /dev/null
+++ b/tests/config/nextflow.config
@@ -0,0 +1,62 @@
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    singularity_pull_docker_container = false
+    test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+}
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '16.GB',
+        time: '1.h'
+    ]
+}
+
+profiles {
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        singularity.registry = 'quay.io'
+    }
+
+    conda {
+        conda.enabled  = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    mamba {
+        conda.enabled  = true
+        conda.useMamba = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    micromamba {
+        conda.enabled  = true
+        conda.useMicromamba = true
+        conda.channels = ['conda-forge', 'bioconda']
+        conda.createTimeout = "120 min"
+    }
+
+    podman {
+        podman.enabled = true
+        podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+        podman.registry = 'quay.io'
+    }
+
+    docker {
+        docker.enabled = true
+        docker.fixOwnership = true
+        docker.runOptions = '--platform=linux/amd64'
+        docker.registry = 'quay.io'
+    }
+}
+
+// Load test_data.config containing paths to test data
+includeConfig 'test_data.config'
+
+manifest {
+    nextflowVersion = '!>=24.10.2'
+}
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
new file mode 100644
index 0000000..3a1cca8
--- /dev/null
+++ b/tests/config/nf-test.config
@@ -0,0 +1,98 @@
+params {
+    publish_dir_mode                  = "copy"
+    singularity_pull_docker_container = false
+    test_data_base                    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+    modules_testdata_base_path        = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+}
+
+process {
+    cpus   = 2
+    memory = '4.GB'
+    time   = '2.h'
+}
+
+profiles {
+    conda {
+        conda.enabled           = true
+        conda.channels          = ['conda-forge', 'bioconda']
+        apptainer.enabled       = false
+    }
+    mamba {
+        conda.enabled           = true
+        conda.useMamba          = true
+    }
+    micromamba {
+        conda.enabled           = true
+        conda.useMicromamba     = true
+    }
+    docker {
+        docker.enabled          = true
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+    docker_self_hosted {
+        docker.enabled          = true
+        docker.fixOwnership     = true
+        docker.runOptions       = '--platform=linux/amd64'
+    }
+    arm64 {
+        process.arch            = 'arm64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/arm64'
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+    singularity {
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+    }
+    podman {
+        podman.enabled          = true
+        podman.runOptions       = "--runtime crun --platform linux/x86_64 --systemd=always"
+    }
+    shifter {
+        shifter.enabled         = true
+    }
+    charliecloud {
+        charliecloud.enabled    = true
+    }
+    apptainer {
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    gitpod {
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
+    }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
+}
+
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Increase time available to build Conda environment
+conda { createTimeout = "120 min" }
+
+// Load test_data.config containing paths to test data
+includeConfig 'test_data.config'
+
+manifest {
+    nextflowVersion = '!>=24.10.2'
+}
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
new file mode 100644
index 0000000..104b8ec
--- /dev/null
+++ b/tests/config/test_data.config
@@ -0,0 +1,904 @@
+// README:
+// https://github.com/nf-core/test-datasets/blob/modules/README.md
+
+params {
+    // Base directory for test data
+    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules"
+
+    test_data {
+        'sarscov2' {
+            'genome' {
+                genome_fasta                                   = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta"
+                genome_fasta_gz                                = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz"
+                genome_fasta_fai                               = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai"
+                genome_fasta_txt_zst                           = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst"
+                genome_dict                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.dict"
+                genome_gff3                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3"
+                genome_gff3_gz                                 = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz"
+                genome_gtf                                     = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gtf"
+                genome_paf                                     = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.paf"
+                genome_sizes                                   = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.sizes"
+                transcriptome_fasta                            = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta"
+                transcriptome_paf                              = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf"
+                proteome_fasta                                 = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta"
+                proteome_fasta_gz                              = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz"
+
+                test_bed                                       = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed"
+                test_bedpe                                     = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bedpe"
+                test_bed_gz                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz"
+                test2_bed                                      = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed"
+                test_bed12                                     = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12"
+                baits_bed                                      = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed"
+                bed_autosql                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as"
+
+                reference_cnn                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn"
+
+                kraken2                                        = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2"
+                kraken2_tar_gz                                 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz"
+
+                kraken2_bracken                                = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken"
+                kraken2_bracken_tar_gz                         = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz"
+
+                kaiju                                          = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju"
+                kaiju_tar_gz                                   = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz"
+
+                kofamscan_profiles_tar_gz                      = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz"
+                kofamscan_ko_list_gz                           = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz"
+
+                metamaps_db                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/db/metamaps_db.tar.gz"
+
+                ncbi_taxmap_zip                                = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
+                taxon_list_txt                                 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
+
+                mmseqs_tar_gz                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz"
+
+                resfinder_tar_gz                               = "${params.test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz"
+
+                all_sites_fas                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas"
+                informative_sites_fas                          = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas"
+
+                contigs_genome_maf_gz                          = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz"
+                contigs_genome_par                             = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par"
+                lastdb_tar_gz                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"
+
+                baits_interval_list                            = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list"
+                targets_interval_list                          = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list"
+                regions_txt                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt"
+                lc_extrap_mr                                   = "${params.test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr"
+            }
+            'illumina' {
+                test_single_end_bam                            = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam"
+                test_single_end_sorted_bam                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam"
+                test_single_end_sorted_bam_bai                 = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai"
+                test_paired_end_bam                            = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam"
+                test_paired_end_sorted_bam                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
+                test_paired_end_sorted_bam_bai                 = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
+                test_paired_end_methylated_bam                 = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam"
+                test_paired_end_methylated_sorted_bam          = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam"
+                test_paired_end_methylated_sorted_bam_bai      = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai"
+                test_unaligned_bam                             = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam"
+
+                test_1_fastq_gz                                = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
+                test_2_fastq_gz                                = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
+                test_interleaved_fastq_gz                      = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz"
+                test_1_fastq_txt_zst                           = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst"
+                test2_1_fastq_gz                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
+                test2_2_fastq_gz                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
+                test_methylated_1_fastq_gz                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz"
+                test_methylated_2_fastq_gz                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
+                test_1_fastq_gz_fastqc_html                    = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html"
+                test_1_fastq_gz_fastqc_zip                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip"
+
+                test_bedgraph                                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
+
+                test_bigwig                                    = "${params.test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig"
+
+                test_wig_gz                                    = "${params.test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz"
+
+                test_baserecalibrator_table                    = "${params.test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
+
+                test_computematrix_mat_gz                      = "${params.test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
+
+                test_bcf                                       = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf"
+
+                test_vcf                                       = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf"
+                test_vcf_gz                                    = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz"
+                test_vcf_gz_tbi                                = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
+                test2_vcf                                      = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf"
+                test2_vcf_gz                                   = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
+                test2_vcf_gz_tbi                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
+                test2_vcf_targets_tsv_gz                       = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz"
+                test3_vcf                                      = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf"
+                test3_vcf_gz                                   = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
+                test3_vcf_gz_tbi                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
+
+                contigs_fasta                                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta"
+                scaffolds_fasta                                = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
+
+                assembly_gfa                                   = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa"
+                assembly_gfa_bgz                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz"
+                assembly_gfa_gz                                = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz"
+                assembly_gfa_zst                               = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst"
+
+                test_single_end_bam_readlist_txt               = "${params.test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
+
+                SRR13255544_tar_gz                             = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
+                SRR11140744_tar_gz                             = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
+            }
+            'nanopore' {
+                test_sorted_bam                                = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam"
+                test_sorted_bam_bai                            = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
+
+                fast5_tar_gz                                   = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz"
+
+                test_fastq_gz                                  = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
+
+		        test2_fastq_gz                                 = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test_2.fastq.gz"
+
+                test_sequencing_summary                        = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
+
+                test2_sequencing_summary                        = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt"
+            }
+            'metagenome' {
+                classified_reads_assignment                    = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
+                kraken_report                                  = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
+                krona_taxonomy                                 = "${params.test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab"
+                seqid2taxid_map                                = "${params.test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map"
+                nodes_dmp                                      = "${params.test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp"
+                names_dmp                                      = "${params.test_data_base}/data/genomics/sarscov2/metagenome/names.dmp"
+                prot_nodes_dmp                                 = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp"
+                prot_names_dmp                                 = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp"
+                prot_accession2taxid_gz                        = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz"
+            }
+        }
+        'mus_musculus' {
+            'genome' {
+                rnaseq_samplesheet                             = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv"
+                rnaseq_genemeta                                = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv"
+                rnaseq_contrasts                               = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv"
+                rnaseq_matrix                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv"
+                rnaseq_lengths                                 = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv"
+                deseq_results                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv"
+                genome_19_fasta                                = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz"
+                genome_19_gtf                                  = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz"
+            }
+            'illumina' {
+                test_1_fastq_gz                                = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz"
+                test_2_fastq_gz                                = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz"
+                genome_config                                  = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json"
+                multiome_lib_csv                               = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv"
+                test_scARC_gex_R1_fastq_gz                     = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz"
+                test_scARC_gex_R2_fastq_gz                     = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz"
+                test_scARC_atac_R1_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz"
+                test_scARC_atac_R2_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz"
+                test_scARC_atac_I2_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz"
+            }
+            'csv' {
+                count_table                                    = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv"
+                library                                        = "${params.test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv"
+            }
+            'txt' {
+                design_matrix                                  = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt"
+            }
+        }
+        'homo_sapiens' {
+            'genome' {
+                'riboseq' {
+                    genome_gtf_20                              = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf"
+                    genome_fasta_20                            = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz"
+                    genome_alignment_bam                       = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam"
+                    genome_alignment_bai                       = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bai"
+                    transcriptome_alignment_bam                = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888.Aligned.toTranscriptome.out.bam"
+                }
+            }
+            '10xgenomics' {
+                cellranger {
+                    test_10x_10k_pbmc_5fb_fastq_1_gz          = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_5fb_fastq_2_gz          = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_5gex_fastq_1_gz         = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_5gex_fastq_2_gz         = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_b_fastq_1_gz            = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_b_fastq_2_gz            = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_t_fastq_1_gz            = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_t_fastq_2_gz            = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_feature_ref_csv         = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv"
+
+                    test_10x_10k_pbmc_cmo_cmo_fastq_1_gz      = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_cmo_fastq_2_gz      = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_gex1_fastq_1_gz     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_gex1_fastq_2_gz     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_gex2_fastq_1_gz     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_gex2_fastq_2_gz     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz"
+                    test_10x_10k_pbmc_cmo_feature_ref_csv     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv"
+
+                    test_10x_5k_cmvpos_tcells_ab_fastq_1_gz   = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_ab_fastq_2_gz   = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz  = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz  = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz"
+                    test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv"
+
+                    test_10x_vdj_ref_json                     = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json"
+                    test_10x_vdj_ref_fasta                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa"
+                    test_10x_vdj_ref_suppfasta                = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa"
+
+                    test_scATAC_1_fastq_gz                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz"
+                    test_scATAC_2_fastq_gz                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz"
+                    test_scATAC_3_fastq_gz                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz"
+                    test_scATAC_I_fastq_gz                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz"
+
+                    test_10x_matrix_rna_raw_h5                = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/438-21-raw_feature_bc_matrix.h5"
+                    test_10x_matrix_hto_csv                   = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/438_21_raw_HTO.csv"
+
+                    test_10x_sc3_v3_5k_a549_gex_l1_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L001_R1_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_gex_l1_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L001_R2_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_gex_l2_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L002_R1_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_gex_l2_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L002_R2_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_crispr_l1_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L001_R1_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_crispr_l1_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L001_R2_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_crispr_l2_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L002_R1_001.fastq.gz"
+                    test_10x_sc3_v3_5k_a549_crispr_l2_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L002_R2_001.fastq.gz"
+
+                }
+                spaceranger {
+                    test_10x_ffpe_cytassist_fastq_1_gz        = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz"
+                    test_10x_ffpe_cytassist_fastq_2_gz        = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz"
+                    test_10x_ffpe_cytassist_image             = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif"
+                    test_10x_ffpe_cytassist_probeset          = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv"
+
+                    test_10x_ffpe_v1_fastq_1_gz               = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz"
+                    test_10x_ffpe_v1_fastq_2_gz               = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz"
+                    test_10x_ffpe_v1_image                    = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
+                }
+            }
+            'genome' {
+                genome_elfasta                                 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta"
+                genome_fasta                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta"
+                genome_fasta_fai                               = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
+                genome_fasta_gz                                = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz"
+                genome_fasta_gz_fai                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai"
+                genome_fasta_gz_gzi                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi"
+                genome_strtablefile                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip"
+                genome_dict                                    = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict"
+                genome_gff3                                    = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3"
+                genome_gtf                                     = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf"
+                genome_interval_list                           = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list"
+                genome_multi_interval_bed                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
+                genome_blacklist_interval_bed                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed"
+                genome_sizes                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes"
+                genome_bed                                     = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed"
+                genome_header                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.header"
+                genome_bed_gz                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz"
+                genome_bed_gz_tbi                              = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
+                genome_elsites                                 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites"
+                transcriptome_fasta                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta"
+                genome2_fasta                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta"
+                genome_chain_gz                                = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz"
+                genome_annotated_interval_tsv                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv"
+                genome_mt_gb                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb"
+                genome_preprocessed_count_tsv                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv"
+                genome_preprocessed_interval_list              = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list"
+                genome_ploidy_model                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz"
+                genome_ploidy_calls                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz"
+                genome_germline_cnv_model                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz"
+                genome_germline_cnv_calls                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz"
+                genome_motifs                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt"
+                genome_config                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json"
+
+                genome_1_fasta                                 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz"
+                genome_1_gtf                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf"
+
+                genome_21_sdf                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz"
+                genome_21_fasta                                = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+                genome_21_fasta_fai                            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+                genome_21_gencode_gtf                          = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf"
+                genome_21_dict                                 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
+                genome_21_sizes                                = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
+                genome_21_interval_list                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
+                genome_21_annotated_bed                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed"
+                genome_21_multi_interval_bed                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
+                genome_21_multi_interval_antitarget_bed        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed"
+                genome_21_multi_interval_bed_gz                = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
+                genome_21_multi_interval_bed_gz_tbi            = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
+                genome_21_chromosomes_dir                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
+                genome_21_reference_cnn                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
+                genome_21_eigenstrat_snp                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp"
+                genome_21_stitch_posfile                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv"
+
+                dbsnp_146_hg38_elsites                         = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
+                dbsnp_146_hg38_vcf_gz                          = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
+                dbsnp_146_hg38_vcf_gz_tbi                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
+                gnomad_r2_1_1_vcf_gz                           = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
+                gnomad_r2_1_1_vcf_gz_tbi                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
+                mills_and_1000g_indels_vcf_gz                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
+                mills_and_1000g_indels_vcf_gz_tbi              = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
+                syntheticvcf_short_vcf_gz                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
+                syntheticvcf_short_vcf_gz_tbi                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
+                syntheticvcf_short_score                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
+                gnomad_r2_1_1_sv_vcf_gz                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
+                gnomad2_r2_1_1_sv_vcf_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz"
+                genmod_compound_vcf_mt                         = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/genmod_compound.vcf"
+
+                hapmap_3_3_hg38_21_vcf_gz                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
+                hapmap_3_3_hg38_21_vcf_gz_tbi                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
+                res_1000g_omni2_5_hg38_21_vcf_gz               = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz"
+                res_1000g_omni2_5_hg38_21_vcf_gz_tbi           = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi"
+                res_1000g_phase1_snps_hg38_21_vcf_gz           = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz"
+                res_1000g_phase1_snps_hg38_21_vcf_gz_tbi       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi"
+                dbsnp_138_hg38_21_vcf_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
+                dbsnp_138_hg38_21_vcf_gz_tbi                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
+                gnomad_r2_1_1_21_vcf_gz                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
+                gnomad_r2_1_1_21_vcf_gz_tbi                    = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
+                mills_and_1000g_indels_21_vcf_gz               = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
+                mills_and_1000g_indels_21_vcf_gz_tbi           = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
+                haplotype_map                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt"
+                dbNSFP_4_1a_21_hg38_txt_gz                     = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz"
+                dbNSFP_4_1a_21_hg38_txt_tbi                    = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi"
+                ngscheckmate_bed                               = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
+
+                index_salmon                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/index/salmon"
+                repeat_expansions                              = "${params.test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
+                justhusky_ped                                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
+                justhusky_minimal_vcf_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
+                justhusky_minimal_vcf_gz_tbi                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
+
+                vcfanno_tar_gz                                 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
+                vcfanno_toml                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
+                updsites_bed                                   = "${params.test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed"
+
+                prg_input                                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip"
+                crispr_functional_counts                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv"
+                crispr_functional_library                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv"
+
+                vep_cache                                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz"
+                affy_array_samplesheet                         = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv"
+                affy_array_celfiles_tar                        = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar"
+
+            }
+            'pangenome' {
+                pangenome_fa                                   = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa"
+                pangenome_fa_bgzip                             = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz"
+                pangenome_fa_bgzip_fai                         = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai"
+                pangenome_fa_bgzip_gzi                         = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi"
+                pangenome_paf                                  = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf"
+                pangenome_paf_gz                               = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz"
+                pangenome_panacus_tsv                          = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv"
+                pangenome_seqwish_gfa                          = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
+                pangenome_smoothxg_gfa                         = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
+                pangenome_gfaffix_gfa                          = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
+                'odgi' {
+                    pangenome_og                               = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og"
+                    pangenome_lay                              = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay"
+                }
+            }
+            'illumina' {
+                test_paired_end_sorted_bam                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
+                test_paired_end_sorted_bam_bai                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
+                test_paired_end_name_sorted_bam                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam"
+                test_paired_end_markduplicates_sorted_bam               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
+                test_paired_end_markduplicates_sorted_bam_bai           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
+                test_paired_end_markduplicates_sorted_referencesn_txt   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
+                test_paired_end_recalibrated_sorted_bam                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
+                test_paired_end_recalibrated_sorted_bam_bai             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
+                test_paired_end_umi_consensus_bam                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
+                test_paired_end_umi_converted_bam                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
+                test_paired_end_umi_grouped_bam                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
+                test_paired_end_umi_histogram_txt                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
+                test_paired_end_umi_unsorted_bam                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
+                test_paired_end_umi_unsorted_tagged_bam                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
+                test_paired_end_hla                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
+                test_paired_end_hla_sorted_bam                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
+                test_paired_end_hla_sorted_bam_bai                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
+                test_rna_paired_end_sorted_chr6_bam                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam"
+                test_rna_paired_end_sorted_chr6_bam_bai                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai"
+
+                test2_paired_end_sorted_bam                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
+                test2_paired_end_sorted_bam_bai                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
+                test2_paired_end_name_sorted_bam                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
+                test2_paired_end_markduplicates_sorted_bam              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
+                test2_paired_end_markduplicates_sorted_bam_bai          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
+                test2_paired_end_recalibrated_sorted_bam                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
+                test2_paired_end_recalibrated_sorted_bam_bai            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
+                test2_paired_end_umi_consensus_bam                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
+                test2_paired_end_umi_converted_bam                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
+                test2_paired_end_umi_grouped_bam                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
+                test2_paired_end_umi_histogram_txt                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
+                test2_paired_end_umi_unsorted_bam                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
+                test2_paired_end_umi_unsorted_tagged_bam                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
+                test_paired_end_duplex_umi_unmapped_bam                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam"
+                test_paired_end_duplex_umi_mapped_bam                   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam"
+                test_paired_end_duplex_umi_mapped_tagged_bam            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam"
+                test_paired_end_duplex_umi_grouped_bam                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam"
+                test_paired_end_duplex_umi_duplex_consensus_bam         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam"
+
+                mitochon_standin_recalibrated_sorted_bam                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
+                mitochon_standin_recalibrated_sorted_bam_bai            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
+                test_illumina_mt_bam                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam"
+                test_illumina_mt_bam_bai                                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai"
+
+                test3_single_end_markduplicates_sorted_bam              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
+
+                read_group_settings_txt                                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt"
+
+                test_paired_end_sorted_cram                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
+                test_paired_end_sorted_cram_crai                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
+                test_paired_end_markduplicates_sorted_cram              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
+                test_paired_end_markduplicates_sorted_cram_crai         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
+                test_paired_end_recalibrated_sorted_cram                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
+                test_paired_end_recalibrated_sorted_cram_crai           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
+
+                test2_paired_end_sorted_cram                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
+                test2_paired_end_sorted_cram_crai                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
+                test2_paired_end_markduplicates_sorted_cram             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
+                test2_paired_end_markduplicates_sorted_cram_crai        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
+                test2_paired_end_recalibrated_sorted_cram               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
+                test2_paired_end_recalibrated_sorted_cram_crai          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
+                test3_paired_end_recalibrated_sorted_cram               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram"
+                test3_paired_end_recalibrated_sorted_cram_crai          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai"
+
+                test_1_fastq_gz                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
+                test_2_fastq_gz                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
+                test_umi_1_fastq_gz                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
+                test_umi_2_fastq_gz                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
+                test_airrseq_1_fastq_gz                                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz"
+                test_airrseq_2_fastq_gz                                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz"
+                test2_1_fastq_gz                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
+                test2_2_fastq_gz                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
+                test2_umi_1_fastq_gz                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
+                test2_umi_2_fastq_gz                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
+                test_rnaseq_1_fastq_gz                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
+                test_rnaseq_2_fastq_gz                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
+                test_paired_end_duplex_umi_1_fastq_gz                   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz"
+                test_paired_end_duplex_umi_2_fastq_gz                   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz"
+
+                test_baserecalibrator_table                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
+                test2_baserecalibrator_table                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
+                test_pileups_table                                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
+                test2_pileups_table                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
+
+                test_paired_end_sorted_dragstrmodel                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
+
+                test_genomicsdb_tar_gz                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
+                test_pon_genomicsdb_tar_gz                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
+
+                test2_haplotc_ann_vcf_gz                                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
+                test2_haplotc_ann_vcf_gz_tbi                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
+                test_haplotc_cnn_vcf_gz                                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz"
+                test_haplotc_cnn_vcf_gz_tbi                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi"
+
+                test2_haplotc_vcf_gz                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz"
+                test2_haplotc_vcf_gz_tbi                                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi"
+
+                test2_recal                                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
+                test2_recal_idx                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
+                test2_tranches                                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
+                test2_allele_specific_recal                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
+                test2_allele_specific_recal_idx                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
+                test2_allele_specific_tranches                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
+
+                test_test2_paired_mutect2_calls_vcf_gz                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
+                test_test2_paired_mutect2_calls_vcf_gz_tbi              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
+                test_test2_paired_mutect2_calls_vcf_gz_stats            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
+                test_test2_paired_mutect2_calls_f1r2_tar_gz             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
+                test_test2_paired_mutect2_calls_artifact_prior_tar_gz   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
+                test_test2_paired_segmentation_table                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
+                test_test2_paired_contamination_table                   = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
+
+                test_genome_vcf                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
+                test_genome_vcf_gz                                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
+                test_genome_vcf_gz_tbi                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
+                test_genome_vcf_idx                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
+
+                test_genome_vcf_ud                                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD"
+                test_genome_vcf_mu                                      = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu"
+                test_genome_vcf_bed                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed"
+
+                test2_genome_vcf                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
+                test2_genome_vcf_gz                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
+                test2_genome_vcf_gz_tbi                                 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
+                test2_genome_vcf_idx                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
+
+                test_genome21_indels_vcf_gz                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
+                test_genome21_indels_vcf_gz_tbi                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
+
+                test_mpileup                                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
+                test2_mpileup                                           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
+
+                test_broadpeak                                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
+                test2_broadpeak                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
+
+                test_narrowpeak                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
+                test2_narrowpeak                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
+
+                test_yak                                                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak"
+                test2_yak                                               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak"
+
+                cutandrun_bedgraph_test_1                               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
+                cutandrun_bedgraph_test_2                               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
+                na24385_chr22_coverage                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed"
+
+                empty_vcf_gz                                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz"
+                empty_vcf_gz_tbi                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi"
+
+                simulated_sv                                            = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz"
+                simulated_sv_tbi                                        = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi"
+                simulated_sv2                                           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz"
+                simulated_sv2_tbi                                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi"
+
+                test_rnaseq_vcf                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
+                test_sv_vcf                                             = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
+                test_sv_vcf_tbi                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi"
+                na24385_chr22_sv_vcf                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz"
+                na24385_chr22_sv_vcf_tbi                                = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi"
+                genmod_vcf_gz                                           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz"
+                genmod_annotate_vcf_gz                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz"
+                genmod_models_vcf_gz                                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz"
+                genmod_score_vcf_gz                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz"
+
+                test_mito_vcf                                           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz"
+
+                test_pytor                                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor"
+                rank_model                                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini"
+
+                test_flowcell                                           = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
+                test_flowcell_samplesheet                               = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv"
+
+                varlociraptor_scenario                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml"
+
+                test_interop_bcl2fastqstats_flowcell                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/interop_bcl2fastqstats/test_flowcell_stats.tar.gz"
+
+                contig_ploidy_priors_table                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
+
+                purecn_ex1_bam                                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam"
+                purecn_ex1_bai                                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai"
+                purecn_ex1_interval                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt"
+                purecn_ex1_normal                                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz"
+                purecn_ex2_normal                                       = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz"
+                purecn_normalpanel_vcf                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz"
+                purecn_normalpanel_tbi                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi"
+            }
+            'lexogen' {
+                i1_read_1                       = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_read_1.fastq.gz"
+                i1_read_2                       = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_read_2.fastq.gz"
+                i1_sample_sheet                 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_sample_sheet.csv"
+                i5_i1_read_1                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_read_1.fastq.gz"
+                i5_i1_read_2                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_read_2.fastq.gz"
+                i5_i1_sample_sheet              = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_sample_sheet.csv"
+                i7_i1_read_1                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_read_1.fastq.gz"
+                i7_i1_read_2                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_read_2.fastq.gz"
+                i7_i1_sample_sheet              = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_sample_sheet.csv"
+                i7_i5_i1_read_1                 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_read_1.fastq.gz"
+                i7_i5_i1_read_2                 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_read_2.fastq.gz"
+                i7_i5_i1_sample_sheet           = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_sample_sheet.csv"
+                i7_i5_read_1                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_read_1.fastq.gz"
+                i7_i5_read_2                    = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_read_2.fastq.gz"
+                i7_i5_sample_sheet              = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_sample_sheet.csv"
+            }
+            'pacbio' {
+                primers                         = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
+                alz                             = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam"
+                alzpbi                          = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
+                ccs                             = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
+                ccs_fa                          = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
+                ccs_fa_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
+                ccs_fq                          = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
+                ccs_fq_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
+                ccs_xml                         = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
+                hifi                            = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
+                lima                            = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
+                refine                          = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
+                cluster                         = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
+                singletons                      = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
+                aligned                         = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
+                alignedbai                      = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
+                genemodel1                      = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
+                genemodel2                      = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
+                filelist                        = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt"
+                tag                             = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam"
+            }
+            'popgen' {
+                plink_case_control_bed          = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bed"
+                plink_case_control_bim          = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bim"
+                plink_case_control_fam          = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.fam"
+                plink_case_control_vcf_gz       = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.vcf.gz"
+                plink_case_control_bcf_gz       = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bcf.gz"
+                plink_simulated_phe             = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.phe"
+                plink_simulated_phenoname       = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe"
+                plink_random_selected_snp       = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_random_selected_snp.txt"
+                plink_simulated_pgen            = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.pgen"
+                plink_simulated_psam            = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.psam"
+                plink_simulated_pvar            = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.pvar"
+            }
+            'scramble' {
+                fasta                           = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa"
+                fasta_fai                       = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai"
+                bam                             = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam"
+                bam_bai                         = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai"
+                cram                            = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram"
+                cram_crai                       = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai"
+                bed                             = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bed"
+            }
+            'gene_set_analysis' {
+                gct                             = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct"
+                cls                             = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls"
+                gmx                             = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx"
+            }
+            'cnvkit' {
+                amplicon_cnr                    = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr"
+                amplicon_cns                    = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns"
+            }
+            'demultiplexing' {
+                bam                             = "${params.test_data_base}/data/genomics/homo_sapiens/demultiplexing/chr21.bam"
+                donor_genotype                  = "${params.test_data_base}/data/genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf"
+            }
+        }
+        'actinidia_chinensis' {
+            'genome' {
+                genome_1_fasta_gz               = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz"
+                genome_1_gff3_gz                = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gff3.gz"
+                genome_1_gtf_gz                 = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz"
+                genome_1_hints_gff_gz           = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.hints.gff.gz"
+            }
+        }
+        'bacteroides_fragilis' {
+            'genome' {
+                genome_fna_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
+                genome_gbff_gz                  = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
+                genome_paf                      = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
+                genome_gff_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz"
+
+            }
+            'hamronization' {
+                genome_abricate_tsv             = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv"
+                genome_mapping_potential_arg    = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG"
+            }
+            'illumina' {
+                test1_contigs_fa_gz             = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
+                test1_1_fastq_gz                = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
+                test1_2_fastq_gz                = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
+                test2_1_fastq_gz                = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
+                test2_2_fastq_gz                = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
+                test1_contigs_sorted_bam        = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam"
+                test1_paired_end_bam            = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam"
+                test1_paired_end_sorted_bam     = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
+                test1_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
+                test2_paired_end_bam            = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam"
+                test2_paired_end_sorted_bam     = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
+                test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
+                test1_contigs_coverage_stats    = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/coverage/test1_contigs.coverage.stats.txt"
+                test1_contigs_ids_tsv           = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/tsv/test1_contigs_ids.tsv"
+            }
+            'nanopore' {
+                test_fastq_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
+                overlap_paf                     = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf"
+            }
+        }
+        'candidatus_portiera_aleyrodidarum' {
+            'genome' {
+                genome_fasta                    = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta"
+                genome_sizes                    = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes"
+                genome_aln_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz"
+                genome_aln_nwk                  = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk"
+                proteome_fasta                  = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta"
+                test1_gff                       = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff"
+                test2_gff                       = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff"
+                test3_gff                       = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
+            }
+            'illumina' {
+                test_1_fastq_gz                 = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz"
+                test_2_fastq_gz                 = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
+                test_se_fastq_gz                = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
+            }
+            'nanopore' {
+                test_fastq_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz"
+            }
+        }
+        'haemophilus_influenzae' {
+            'genome' {
+                genome_fna_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz"
+                genome_aln_gz                   = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz"
+                genome_aln_nwk                  = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
+            }
+        }
+        'metagenome' {
+            'taxonomy' {
+                sink_taxid_csv                   = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sink_taxid.csv"
+                sources_taxid_csv                = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sources_labels.csv"
+                sources_labels_csv               = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sources_taxid.csv"
+                taxa_sqlite 	                 = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite.xz"
+                taxa_sqlite_traverse_pkl         = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite_traverse.pkl"
+            }
+        }
+        'streptococcus_agalactiae' {
+            'genome' {
+                emu_db                           = "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/genome/emu"
+                }
+            'nanopore' {
+                test_fastq_gz                    =  "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/nanopore/fastq/test.fastq.gz"
+                }
+        }
+        'saccharomyces_cerevisiae' {
+            'genome' {
+                samplesheet                     = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv"
+                genome_gfp_gtf                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf"
+		        kallisto_results                = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
+                salmon_results                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz"
+            }
+        }
+        'generic' {
+            'csv' {
+                test_csv                        = "${params.test_data_base}/data/generic/csv/test.csv"
+            }
+            'notebooks' {
+                rmarkdown                       = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
+                ipython_md                      = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md"
+                ipython_ipynb                   = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb"
+                quarto_r                        = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_r.qmd"
+                quarto_python                   = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_python.qmd"
+            }
+            'tar' {
+                tar_gz                          = "${params.test_data_base}/data/generic/tar/hello.tar.gz"
+            }
+            'tsv' {
+                test_tsv                        = "${params.test_data_base}/data/generic/tsv/test.tsv"
+                expression                      = "${params.test_data_base}/data/generic/tsv/expression.tsv"
+                network                         = "${params.test_data_base}/data/generic/tsv/network.tsv"
+            }
+            'txt' {
+                hello                           = "${params.test_data_base}/data/generic/txt/hello.txt"
+            }
+            'cooler'{
+                test_pairix_pair_gz             = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
+                test_pairix_pair_gz_px2         = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
+                test_pairs_pair                 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
+                test_tabix_pair_gz              = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
+                test_tabix_pair_gz_tbi          = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
+                hg19_chrom_sizes                = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
+                test_merge_cool                 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
+                test_merge_cool_cp2             = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
+
+            }
+            'pairtools' {
+                mock_4dedup_pairsam             = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam"
+                mock_4flip_pairs                = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs"
+                mock_chrom_sizes                = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes"
+                mock_pairsam                    = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam"
+                mock_sam                        = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam"
+                frag_bed                        = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed"
+            }
+            'estsfs'{
+                config_file                     = "${params.test_data_base}/data/delete_me/estsfs/config-JC.txt"
+                data_file                       = "${params.test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT"
+                seed_file                       = "${params.test_data_base}/data/delete_me/estsfs/seedfile.txt"
+            }
+            'config' {
+                agat_config                     = "${params.test_data_base}/data/generic/config/agat_config.yaml"
+                config_network_datavzrd         = "${params.test_data_base}/data/generic/config/config_network.datavzrd.yaml"
+                config_test_datavzrd            = "${params.test_data_base}/data/generic/config/config_test.datavzrd.yaml"
+                ncbi_user_settings              = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
+                wittyer_config                  = "${params.test_data_base}/data/generic/config/wittyer_config.json"
+            }
+            'unsorted_data' {
+                'unsorted_text' {
+                    genome_file                 = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome"
+                    intervals                   = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed"
+                    numbers_csv                 = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv"
+                    }
+            }
+        }
+        'proteomics' {
+            'msspectra' {
+                ups_file1                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw"
+                ups_file2                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw"
+                profile_spectra                 = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML"
+                hla2_file                       = "${params.test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw"
+            }
+            'database' {
+                yeast_ups                       = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta"
+                swissprot                       = "${params.test_data_base}/data/proteomics/database/UP000005640_9606.fasta"
+            }
+            'maxquant' {
+                mq_contrasts                    = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv"
+                mq_proteingroups                = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt"
+                mq_samplesheet                  = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv"
+                mq_proteus_mat                  = "${params.test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv"
+            }
+            'parameter' {
+                maxquant                        = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml"
+		        sage_base_config                = "${params.test_data_base}/data/proteomics/parameter/sage_base_config.json"
+            }
+            'openms' {
+                idxml1                          = "${params.test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML"
+                idxml2                          = "${params.test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML"
+            }
+            'pdb' {
+                tim1_pdb                        = "${params.test_data_base}/data/proteomics/pdb/1tim.pdb"
+                tim8_pdb                        = "${params.test_data_base}/data/proteomics/pdb/8tim.pdb"
+            }
+        }
+        'galaxea_fascicularis' {
+            hic {
+                pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext"
+            }
+        }
+        'deilephila_porcellus' {
+            'mito' {
+                ref_fa      = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta"
+                ref_gb      = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb"
+                hifi_reads  = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa"
+                contigs     = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa"
+            }
+        }
+        'arabidopsis_thaliana' {
+            'plastid' {
+                hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta"
+            }
+        }
+
+        'imaging' {
+            'h5' {
+                plant_wga                       = "${params.test_data_base}/data/imaging/h5/plant_wga.h5"
+                plant_wga_prob                  = "${params.test_data_base}/data/imaging/h5/plant_wga_probabilities.h5"
+            }
+            'ilp' {
+                plant_wga_multicut              = "${params.test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp"
+                plant_wga_pixel_class           = "${params.test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp"
+            }
+            'tiff' {
+                mouse_heart_wga                 = "${params.test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff"
+            }
+            'ome-tiff' {
+                cycif_tonsil_channels   = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv"
+                cycif_tonsil_cycle1     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif"
+                cycif_tonsil_cycle2     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif"
+                cycif_tonsil_cycle3     = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif"
+                cycif_tonsil_dfp        = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif"
+                cycif_tonsil_ffp        = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif"
+            }
+            'registration' {
+                markers                 = "${params.test_data_base}/data/imaging/registration/markers.csv"
+                cycle1                  = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif"
+                cycle2                  = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif"
+            }
+            'segmentation' {
+                markers                 = "${params.test_data_base}/data/imaging/segmentation/markers.csv"
+                image                   = "${params.test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif"
+                nuclear_image           = "${params.test_data_base}/data/imaging/segmentation/nuclear_image.tif"
+            }
+            'quantification' {
+                markers                 = "${params.test_data_base}/data/imaging/quantification/markers.csv"
+                image                   = "${params.test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif"
+                mask                    = "${params.test_data_base}/data/imaging/quantification/cell.ome.tif"
+            }
+            'downstream' {
+                markers                 = "${params.test_data_base}/data/imaging/downstream/markers.csv"
+                cell_feature_array      = "${params.test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv"
+                phenotyped              = "${params.test_data_base}/data/imaging/downstream/phenotyped.csv"
+                    'celesta' {
+                        data            = "${params.test_data_base}/data/imaging/downstream/celesta/img_data.csv"
+                        signature       = "${params.test_data_base}/data/imaging/downstream/celesta/signature_matrix.csv"
+                        thresholds      = "${params.test_data_base}/data/imaging/downstream/celesta/thresholds_celesta.csv"
+                    }
+            }
+            'background_subtraction' {
+                markers                 = "${params.test_data_base}/data/imaging/background_subtraction/markers.csv"
+                image                   = "${params.test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif"
+            }
+            'core_detection' {
+                image                   = "${params.test_data_base}/data/imaging/core_detection/single_core_dapi.tif"
+            }
+            'spot_detection' {
+                image                   = "${params.test_data_base}/data/imaging/spot_detection/immunofluorescence.tif"
+            }
+            'staging' {
+                folder                  = "${params.test_data_base}/data/imaging/staging/phenoimager/"
+                file1                   = "${params.test_data_base}/data/imaging/staging/phenoimager/tile1.tif"
+                file2                   = "${params.test_data_base}/data/imaging/staging/phenoimager/tile2.tif"
+            }
+            'imc_staging' {
+                text                    = "${params.test_data_base}/data/imaging/staging/imaging_mass_cytometry/acquisition.txt"
+            }
+        }
+    }
+}