diff --git a/.github/check_duplicate_md5s.py b/.github/check_duplicate_md5s.py
new file mode 100644
index 0000000..60506ab
--- /dev/null
+++ b/.github/check_duplicate_md5s.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+from rich import print
+from rich.table import Table
+import click
+import glob
+import os
+import yaml
+
+
+@click.command()
+@click.option(
+    "--min_dups",
+    default=5,
+    show_default=True,
+    help="Minimum number of duplicates to report",
+)
+@click.option(
+    "--search_dir",
+    default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
+    show_default=True,
+    help="Glob directory pattern used to find test YAML files",
+)
+def find_duplicate_md5s(min_dups, search_dir):
+    """
+    Find duplicate file MD5 sums in test YAML files.
+    """
+    md5_filenames = {}
+    md5_output_fn_counts = {}
+    module_counts = {}
+
+    # Loop through all files in tests/ called test.yml
+    for test_yml in glob.glob(search_dir, recursive=True):
+        # Open file and parse YAML
+        with open(test_yml, "r") as fh:
+            test_config = yaml.safe_load(fh)
+            # Loop through tests and check for duplicate md5s
+            for test in test_config:
+                for test_file in test.get("files", []):
+                    if "md5sum" in test_file:
+                        md5 = test_file["md5sum"]
+                        md5_filenames[md5] = md5_filenames.get(md5, []) + [
+                            os.path.basename(test_file.get("path"))
+                        ]
+                        md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
+                        # Log the module that this md5 was in
+                        modname = os.path.basename(os.path.dirname(test_yml))
+                        # If tool/subtool show the whole thing
+                        # Ugly code but trying to stat os-agnostic
+                        if os.path.basename(
+                            os.path.dirname(os.path.dirname(test_yml))
+                        ) not in ["modules", "config", "subworkflows"]:
+                            modname = "{}/{}".format(
+                                os.path.basename(
+                                    os.path.dirname(os.path.dirname(test_yml))
+                                ),
+                                os.path.basename(os.path.dirname(test_yml)),
+                            )
+                        module_counts[md5] = module_counts.get(md5, []) + [modname]
+
+    # Set up rich table
+    table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
+    table.add_column("MD5", style="cyan", no_wrap=True)
+    table.add_column("Count", style="magenta", justify="right")
+    table.add_column("Num modules", style="blue", justify="right")
+    table.add_column("Filenames", style="green")
+
+    # Add rows - sort md5_output_fn_counts by value
+    for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
+        if md5_output_fn_counts[md5] >= min_dups:
+            table.add_row(
+                md5,
+                str(md5_output_fn_counts[md5]),
+                str(len(set(module_counts[md5]))),
+                ", ".join(set(md5_filenames[md5])),
+            )
+
+    print(table)
+
+
+if __name__ == "__main__":
+    find_duplicate_md5s()
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
new file mode 100644
index 0000000..37beaa8
--- /dev/null
+++ b/.github/workflows/fix-linting.yml
@@ -0,0 +1,72 @@
+name: fix-linting
+run-name: fix linting (automated)
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  fix-linting:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '/fix linting') &&
+      (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') &&
+      github.repository == 'CCBR/nf-modules'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_PAT }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Post nothing-to-do comment
+        if: steps.prettier_status.outputs.result == 'pass'
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            Nothing for me to do here! :shrug:
+            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "🤖 Fix linting with Prettier"
+          git push
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..c450704
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,307 @@
+name: test
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  merge_group:
+    types: [checks_requested]
+    branches: [main]
+
+# 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
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  pytest-changes:
+    name: pytest-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+          token: "${{ secrets.GITHUB_TOKEN }}"
+
+  nf-core-lint:
+    runs-on: ubuntu-20.04
+    name: nf-core-lint
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        exclude:
+          - tags: "nf-test"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        if: ${{ !startsWith(matrix.tags, 'subworkflows/') }}
+
+      - name: Remove substring from matrix.tags
+        id: remove_substring
+        run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT
+
+      - name: Lint subworkflow ${{ matrix.tags }}
+        run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}}
+        if: ${{ startsWith(matrix.tags, 'subworkflows/') }}
+
+  pytest:
+    runs-on: ubuntu-20.04
+    name: pytest
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        profile: ["docker"] #, "singularity", "conda"]
+    env:
+      NXF_ANSI_LOG: false
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography
+
+      - name: Setup Nextflow ${{ matrix.NXF_VER }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@v6
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
+            !${{ github.workspace }}/.singularity
+
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/nftest_modules.yml"
+          token: "${{ secrets.GITHUB_TOKEN }}"
+
+  nf-test:
+    runs-on: ubuntu-20.04
+    name: nf-test
+    needs: [nf-test-changes]
+    if: needs.nf-test-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
+        profile: ["docker"] #, "singularity", "conda"]
+    env:
+      NXF_ANSI_LOG: false
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs:
+      [prettier, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    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/.gitignore b/.gitignore
index a5075df..3189ded 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,14 @@
+*.code-workspace
+*.pyc
+*.pyo
+.*.sw?
+.DS_Store
 .nextflow*
-*.log
+.nf-test/
+.screenrc
+__pycache__
+output/
+results/
+test_output/
+tests/data/
+work/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 676d76b..1e3630c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,3 +2,5 @@
 
 - new modules:
   - cutadapt
+  - bwa/index
+  - bwa/mem
diff --git a/README.md b/README.md
index a9b106f..d4398ff 100644
--- a/README.md
+++ b/README.md
@@ -36,4 +36,5 @@ Many of the modules and subworkflows in this project reuse and adapt code from [
 In those cases, credit is noted in the `meta.yml` file of the module/subworkflow and also listed here:
 
 - [cutadapt](modules/CCBR/cutadapt) adapts the [nf-core cutadapt module](https://github.com/nf-core/modules/tree/master/modules/nf-core/cutadapt)
-- [bwa_mem](modules/CCBR/bwa/mem) adapts the [nf-core bwa-mem module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa/mem)
+- [bwa_mem](modules/CCBR/bwa/mem) adapts the [nf-core bwa mem module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa/mem)
+- [bwa_index](modules/CCBR/bwa/index) adapts the [nf-core bwa index module](https://github.com/nf-core/chipseq/tree/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/nf-core/modules/bwa/index)
diff --git a/modules/CCBR/bwa/index/main.nf b/modules/CCBR/bwa/index/main.nf
new file mode 100644
index 0000000..a30f3d7
--- /dev/null
+++ b/modules/CCBR/bwa/index/main.nf
@@ -0,0 +1,47 @@
+process BWA_INDEX {
+    tag { fasta }
+    label 'process_single'
+
+    container 'nciccbr/ccbr_ubuntu_base_20.04:v5'
+
+    input:
+        tuple val(meta), path(fasta)
+
+    output:
+        tuple val(meta), path(bwa) , emit: index
+        path "versions.yml"        , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    def args   = task.ext.args ?: ''
+    """
+    mkdir bwa
+    bwa \\
+        index \\
+        ${args} \\
+        -p bwa/${prefix} \\
+        ${fasta}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    """
+    mkdir bwa
+    for ext in amb ann bwt pac sa; do
+        touch bwa/${prefix}.\$ext
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/CCBR/bwa/index/meta.yml b/modules/CCBR/bwa/index/meta.yml
new file mode 100644
index 0000000..02a1412
--- /dev/null
+++ b/modules/CCBR/bwa/index/meta.yml
@@ -0,0 +1,41 @@
+name: bwa_index
+description: Create BWA index for reference genome. Adapted from the nf-core bwa index module.
+keywords:
+  - index
+  - fasta
+  - genome
+  - reference
+tools:
+  - bwa:
+      description: |
+        BWA is a software package for mapping DNA sequences against
+        a large reference genome, such as the human genome.
+      homepage: http://bio-bwa.sourceforge.net/
+      documentation: http://www.htslib.org/doc/samtools.html
+      arxiv: arXiv:1303.3997
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Input genome fasta file
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
+  - index:
+      type: file
+      description: BWA genome index files
+      pattern: "*.{amb,ann,bwt,pac,sa}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@kelly-sovacool"
diff --git a/modules/CCBR/bwa/mem/main.nf b/modules/CCBR/bwa/mem/main.nf
index cb9c2b5..4a8fd26 100644
--- a/modules/CCBR/bwa/mem/main.nf
+++ b/modules/CCBR/bwa/mem/main.nf
@@ -2,18 +2,20 @@ process BWA_MEM {
     tag { meta.id }
     label 'process_higher'
 
-    container = 'nciccbr/ccbr_ubuntu_base_20.04:v5'
+    container 'nciccbr/ccbr_ubuntu_base_20.04:v5'
 
     input:
         tuple val(meta), path(fastq)
-        path(index_files)
-        val(index_name)
+        tuple val(meta_idx), path(index_files)
 
     output:
         tuple val(meta), path("*.bam"), emit: bam
         path  "versions.yml"          , emit: versions
 
-    script: 
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     # current working directory is a tmpdir when 'scratch' is set
@@ -21,18 +23,20 @@ process BWA_MEM {
     mkdir \$TMP
     trap 'rm -rf "\$TMP"' EXIT
 
-    bwa mem -t ${task.cpus} ${index_name} ${fastq} -o \$TMP/align.bam
-    
+    INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
+
+    bwa mem -t ${task.cpus} \$INDEX ${fastq} -o \$TMP/align.bam
+
     samtools sort \\
       -@ ${task.cpus} \\
       -m 2G \\
       -T \$TMP \\
       \$TMP/align.bam > ${prefix}.bam
-    
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/modules/CCBR/cutadapt/main.nf b/modules/CCBR/cutadapt/main.nf
index 9848ed8..e4a758f 100644
--- a/modules/CCBR/cutadapt/main.nf
+++ b/modules/CCBR/cutadapt/main.nf
@@ -2,19 +2,18 @@ process CUTADAPT {
     tag { meta.id }
     label 'process_high'
 
-    conda "bioconda::cutadapt=3.4"
     container 'nciccbr/ncigb_cutadapt_v1.18:latest'
 
     input:
-    tuple val(meta), path(reads)
+        tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.trim.fastq.gz'), emit: reads
-    tuple val(meta), path('*.log')          , emit: log
-    path "versions.yml"                     , emit: versions
+        tuple val(meta), path('*.trim.fastq.gz'), emit: reads
+        tuple val(meta), path('*.log')          , emit: log
+        path "versions.yml"                     , emit: versions
 
     when:
-    task.ext.when == null || task.ext.when
+        task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: [
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
new file mode 100644
index 0000000..ca49950
--- /dev/null
+++ b/tests/config/nextflow.config
@@ -0,0 +1,44 @@
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    singularity_pull_docker_container = true
+    test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+}
+
+process {
+    cpus = 2
+    memory = 3.GB
+    time = 2.h
+}
+
+if ("$PROFILE" == "singularity") {
+    singularity.enabled = true
+    singularity.autoMounts = true
+} else if ("$PROFILE" == "conda") {
+    conda.enabled = true
+} else if ("$PROFILE" == "mamba") {
+    conda.enabled  = true
+    conda.useMamba = true
+} else if ("$PROFILE" == "podman") {
+    podman.enabled = true
+    podman.userEmulation = true
+    podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+} else {
+    docker.enabled = true
+    docker.userEmulation = true
+    docker.runOptions = "--platform linux/x86_64"
+}
+
+docker.registry = 'docker.io'
+podman.registry = 'docker.io'
+singularity.registry = 'docker.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 = '!>=23.04.0'
+}
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
new file mode 100644
index 0000000..9254901
--- /dev/null
+++ b/tests/config/nf-test.config
@@ -0,0 +1,49 @@
+params {
+    publish_dir_mode = "copy"
+    singularity_pull_docker_container = true
+    test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules'
+}
+
+process {
+    cpus = 2
+    memory = 3.GB
+    time = 2.h
+}
+
+profiles {
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+    }
+    conda {
+        conda.enabled = true
+    }
+    mamba {
+        conda.enabled  = true
+        conda.useMamba = true
+    }
+    podman {
+        podman.enabled = true
+        podman.userEmulation = true
+        podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+    }
+    docker {
+        docker.enabled = true
+        docker.userEmulation = true
+        docker.runOptions = "--platform linux/x86_64"
+    }
+}
+
+docker.registry = 'docker.io'
+podman.registry = 'docker.io'
+singularity.registry = 'docker.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 = '!>=23.04.0'
+}
diff --git a/tests/config/nftest_modules.yml b/tests/config/nftest_modules.yml
new file mode 100644
index 0000000..1654878
--- /dev/null
+++ b/tests/config/nftest_modules.yml
@@ -0,0 +1,5 @@
+fastqc:
+  - modules/nf-core/fastqc/**
+
+snakemake:
+  - modules/nf-core/snakemake/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
new file mode 100644
index 0000000..f079ab3
--- /dev/null
+++ b/tests/config/pytest_modules.yml
@@ -0,0 +1,11 @@
+bwa/index:
+  - modules/CCBR/bwa/index/**
+  - tests/modules/CCBR/bwa/index/**
+
+bwa/mem:
+  - modules/CCBR/bwa/mem/**
+  - tests/modules/CCBR/bwa/mem/**
+
+cutadapt:
+  - modules/CCBR/cutadapt/**
+  - tests/modules/CCBR/cutadapt/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
new file mode 100644
index 0000000..1c9ed34
--- /dev/null
+++ b/tests/config/test_data.config
@@ -0,0 +1,713 @@
+// 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                            = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta"
+                proteome_fasta                                 = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta"
+                transcriptome_paf                              = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf"
+
+                test_bed                                       = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed"
+                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"
+
+                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                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz"
+
+                all_sites_fas                                  = "${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                                    = "${params.test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt"
+            }
+            'illumina' {
+                test_single_end_bam                            = "${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                     = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
+
+                test_bedgraph                                  = "${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"
+
+                test_sequencing_summary                        = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
+            }
+            'metagenome' {
+                classified_reads_assignment                    = "${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                                      = "${params.test_data_base}/data/genomics/sarscov2/metagenome/names.dmp"
+            }
+        }
+        'mus_musculus' {
+            'genome' {
+                rnaseq_samplesheet                             = "${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                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv"
+                deseq_results                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv"
+            }
+            '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"
+            }
+            '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                                  = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt"
+            }
+        }
+        'homo_sapiens' {
+            '10xgenomics' {
+                cellranger {
+                    test_10x_10k_pbmc_5fb_fastq_1_gz          = "${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                = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa"
+                }
+                spaceranger {
+                    test_10x_ffpe_cytassist_fastq_1_gz        = "${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_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"
+
+                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                    = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi"
+
+                index_salmon                                   = "${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                               = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz"
+                pangenome_seqwish_gfa                          = "${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                                     = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
+                test2_1_fastq_gz                                        = "${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"
+
+                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"
+
+                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                                         = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi"
+                genmod_vcf_gz                                           = "${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                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml"
+
+                contig_ploidy_priors_table                              = "${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                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi"
+            }
+            'pacbio' {
+                primers                         = "${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"
+            }
+            '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"
+            }
+        }
+        '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                = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
+                test1_paired_end_bam            = "${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 = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
+            }
+            'nanopore' {
+                test_fastq_gz                   = "${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"
+            }
+        }
+        '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"
+            }
+            '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"
+            }
+            '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                        = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed"
+            }
+            'config' {
+                ncbi_user_settings              = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
+            }
+            '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                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw"
+            }
+            'database' {
+                yeast_ups                       = "${params.test_data_base}/data/proteomics/database/yeast_UPS.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                        = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml"
+            }
+            'idfile' {
+                openms_idxml                    = "${params.test_data_base}/data/proteomics/openms_idxml/BSA_QC_file.idXML"
+            }
+        }
+        '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     = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa"
+            }
+        }
+        'imaging' {
+            'h5' {
+                plant_wga                       = "${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                   = "${params.test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif"
+            }
+            'quantification' {
+                markers                 = "${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"
+            }
+            '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                   = "${params.test_data_base}/data/imaging/core_detection/single_core_dapi.tif"
+            }
+        }
+    }
+}
diff --git a/tests/modules/CCBR/bwa/index/main.nf b/tests/modules/CCBR/bwa/index/main.nf
new file mode 100644
index 0000000..eb13002
--- /dev/null
+++ b/tests/modules/CCBR/bwa/index/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/CCBR/bwa/index/main.nf'
+
+workflow test_bwa_index {
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BWA_INDEX ( fasta )
+}
diff --git a/tests/modules/CCBR/bwa/index/nextflow.config b/tests/modules/CCBR/bwa/index/nextflow.config
new file mode 100644
index 0000000..8730f1c
--- /dev/null
+++ b/tests/modules/CCBR/bwa/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/CCBR/bwa/index/test.yml b/tests/modules/CCBR/bwa/index/test.yml
new file mode 100644
index 0000000..76cd68f
--- /dev/null
+++ b/tests/modules/CCBR/bwa/index/test.yml
@@ -0,0 +1,30 @@
+- name: bwa index test_bwa_index
+  command: nextflow run ./tests/modules/CCBR/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/bwa/index/nextflow.config
+  tags:
+    - bwa
+    - bwa/index
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/versions.yml
+
+- name: bwa index test_bwa_index_stub
+  command: nextflow run ./tests/modules/CCBR/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/bwa/index/nextflow.config -stub
+  tags:
+    - bwa
+    - bwa/index
+  files:
+    - path: output/bwa/bwa/genome.amb
+    - path: output/bwa/bwa/genome.ann
+    - path: output/bwa/bwa/genome.bwt
+    - path: output/bwa/bwa/genome.pac
+    - path: output/bwa/bwa/genome.sa
+    - path: output/bwa/versions.yml
diff --git a/tests/modules/CCBR/bwa/mem/main.nf b/tests/modules/CCBR/bwa/mem/main.nf
new file mode 100644
index 0000000..f68a0d7
--- /dev/null
+++ b/tests/modules/CCBR/bwa/mem/main.nf
@@ -0,0 +1,85 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../../../modules/CCBR/bwa/index/main.nf'
+include { BWA_MEM   } from '../../../../../modules/CCBR/bwa/mem/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_bwa_mem_single_end {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwa_mem_paired_end {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index )
+}
+
+//
+// Test with stub pairedend
+//
+workflow test_bwa_mem_paired_end_stub {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index )
+}
+
+
+//
+// Test with single-end data stub
+//
+workflow test_bwa_mem_single_end_stub {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = [
+        [id: 'test'],
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BWA_INDEX ( fasta )
+    BWA_MEM ( input, BWA_INDEX.out.index )
+}
diff --git a/tests/modules/CCBR/bwa/mem/nextflow.config b/tests/modules/CCBR/bwa/mem/nextflow.config
new file mode 100644
index 0000000..6d85453
--- /dev/null
+++ b/tests/modules/CCBR/bwa/mem/nextflow.config
@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+
+}
diff --git a/tests/modules/CCBR/bwa/mem/test.yml b/tests/modules/CCBR/bwa/mem/test.yml
new file mode 100644
index 0000000..cac9af0
--- /dev/null
+++ b/tests/modules/CCBR/bwa/mem/test.yml
@@ -0,0 +1,79 @@
+- name: bwa mem test_bwa_mem_single_end
+  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: 6ffda8891403de484a9acd0b23d88076
+    - path: output/bwa/versions.yml
+
+- name: bwa mem test_bwa_mem_paired_end
+  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: 878426eb49302dabb3d3be3dadcbcd9e
+    - path: output/bwa/versions.yml
+
+- name: bwa mem test_bwa_mem_paired_end_stub
+  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_paired_end_stub -c ./tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: 878426eb49302dabb3d3be3dadcbcd9e
+    - path: output/bwa/versions.yml
+
+- name: bwa mem test_bwa_mem_single_end_stub
+  command: nextflow run ./tests/modules/CCBR/bwa/mem -entry test_bwa_mem_single_end_stub -c ./tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa/mem
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: 6ffda8891403de484a9acd0b23d88076
+    - path: output/bwa/versions.yml
diff --git a/tests/modules/CCBR/cutadapt/main.nf b/tests/modules/CCBR/cutadapt/main.nf
new file mode 100644
index 0000000..ce96020
--- /dev/null
+++ b/tests/modules/CCBR/cutadapt/main.nf
@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CUTADAPT } from '../../../../modules/CCBR/cutadapt/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_cutadapt_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    CUTADAPT ( input )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_cutadapt_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    CUTADAPT ( input )
+}
diff --git a/tests/modules/CCBR/cutadapt/nextflow.config b/tests/modules/CCBR/cutadapt/nextflow.config
new file mode 100644
index 0000000..2af532c
--- /dev/null
+++ b/tests/modules/CCBR/cutadapt/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: CUTADAPT {
+        ext.args = '-q 25'
+    }
+
+}
diff --git a/tests/modules/CCBR/cutadapt/test.yml b/tests/modules/CCBR/cutadapt/test.yml
new file mode 100644
index 0000000..155f4b0
--- /dev/null
+++ b/tests/modules/CCBR/cutadapt/test.yml
@@ -0,0 +1,33 @@
+- name: cutadapt single-end
+  command: nextflow run ./tests/modules/CCBR/cutadapt/main.nf -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/cutadapt/nextflow.config
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test.trim.fastq.gz
+
+- name: cutadapt single-end stub
+  command: nextflow run ./tests/modules/CCBR/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/cutadapt/nextflow.config -stub-run
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test.trim.fastq.gz
+
+- name: cutadapt paired-end
+  command: nextflow run ./tests/modules/CCBR/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/cutadapt/nextflow.config
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test_1.trim.fastq.gz
+    - path: ./output/cutadapt/test_2.trim.fastq.gz
+
+- name: cutadapt paired-end stub
+  command: nextflow run ./tests/modules/CCBR/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/CCBR/cutadapt/nextflow.config -stub-run
+  tags:
+    - cutadapt
+  files:
+    - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/test_1.trim.fastq.gz
+    - path: ./output/cutadapt/test_2.trim.fastq.gz