diff --git a/.github/include.yaml b/.github/include.yaml
new file mode 100644
index 0000000..a3629f4
--- /dev/null
+++ b/.github/include.yaml
@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json
diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
deleted file mode 100644
index c0c6175..0000000
--- a/.github/python/find_changed_files.py
+++ /dev/null
@@ -1,317 +0,0 @@
-#!/usr/bin/env python
-
-# This script is used to identify *.nf.test files for changed functions/processs/workflows/pipelines and *.nf-test files
-# with changed dependencies, then return as a JSON list
-
-import argparse
-import json
-import logging
-import re
-import yaml
-
-from itertools import chain
-from pathlib import Path
-from git import Repo
-
-
-def parse_args() -> argparse.Namespace:
-    """
-    Parse command line arguments and return an ArgumentParser object.
-
-    Returns:
-        argparse.ArgumentParser: The ArgumentParser object with the parsed arguments.
-    """
-    parser = argparse.ArgumentParser(
-        description="Scan *.nf.test files for function/process/workflow name and return as a JSON list"
-    )
-    parser.add_argument(
-        "-r",
-        "--head_ref",
-        required=True,
-        help="Head reference branch (Source branch for a PR).",
-    )
-    parser.add_argument(
-        "-b",
-        "--base_ref",
-        required=True,
-        help="Base reference branch (Target branch for a PR).",
-    )
-    parser.add_argument(
-        "-x",
-        "--ignored_files",
-        nargs="+",
-        default=[
-            ".git/*",
-            ".gitpod.yml",
-            ".prettierignore",
-            ".prettierrc.yml",
-            "*.md",
-            "*.png",
-            "modules.json",
-            "pyproject.toml",
-            "tower.yml",
-        ],
-        help="List of files or file substrings to ignore.",
-    )
-    parser.add_argument(
-        "-i",
-        "--include",
-        type=Path,
-        default=".github/python/include.yaml",
-        help="Path to an include file containing a YAML of key value pairs to include in changed files. I.e., return the current directory if an important file is changed.",
-    )
-    parser.add_argument(
-        "-l",
-        "--log-level",
-        choices=["DEBUG", "INFO", "WARNING", "ERROR"],
-        default="INFO",
-        help="Logging level",
-    )
-    parser.add_argument(
-        "-t",
-        "--types",
-        nargs="+",
-        choices=["function", "process", "workflow", "pipeline"],
-        default=["function", "process", "workflow", "pipeline"],
-        help="Types of tests to include.",
-    )
-    return parser.parse_args()
-
-
-def read_yaml_inverted(file_path: str) -> dict:
-    """
-    Read a YAML file and return its contents as a dictionary but reversed, i.e. the values become the keys and the keys become the values.
-
-    Args:
-        file_path (str): The path to the YAML file.
-
-    Returns:
-        dict: The contents of the YAML file as a dictionary inverted.
-    """
-    with open(file_path, "r") as f:
-        data = yaml.safe_load(f)
-
-    # Invert dictionary of lists into contents of lists are keys, values are the original keys
-    # { "key": ["item1", "item2] } --> { "item1": "key", "item2": "key" }
-    return {value: key for key, values in data.items() for value in values}
-
-
-def find_changed_files(
-    branch1: str,
-    branch2: str,
-    ignore: list[str],
-) -> list[Path]:
-    """
-    Find all *.nf.tests that are associated with files that have been changed between two specified branches.
-
-    Args:
-        branch1 (str)      : The first branch being compared
-        branch2 (str)      : The second branch being compared
-        ignore  (list)     : List of files or file substrings to ignore.
-
-    Returns:
-        list: List of files matching the pattern *.nf.test that have changed between branch2 and branch1.
-    """
-    # create repo
-    repo = Repo(".")
-    # identify commit on branch1
-    branch1_commit = repo.commit(branch1)
-    # identify commit on branch2
-    branch2_commit = repo.commit(branch2)
-    # compare two branches
-    diff_index = branch1_commit.diff(branch2_commit)
-
-    # Start empty list of changed files
-    changed_files = []
-
-    # For every file that has changed between commits
-    for file in diff_index:
-        # Get pathlib.Path object
-        filepath = Path(file.a_path)
-        # If file does not match any in the ignore list, add containing directory to changed_files
-        if not any(filepath.match(ignored_path) for ignored_path in ignore):
-            changed_files.append(filepath)
-
-    # Uniqueify the results before returning for efficiency
-    return list(set(changed_files))
-
-
-def detect_include_files(
-    changed_files: list[Path], include_files: dict[str, str]
-) -> list[Path]:
-    """
-    Detects the include files based on the changed files.
-
-    Args:
-        changed_files (list[Path]): List of paths to the changed files.
-        include_files (dict[str, str]): Key-value pairs to return if a certain file has changed. If a file in a directory has changed, it points to a different directory.
-
-    Returns:
-        list[Path]: List of paths to representing the keys of the include_files dictionary, where a value matched a path in changed_files.
-    """
-    new_changed_files = []
-    for filepath in changed_files:
-        # If file is in the include_files, we return the key instead of the value
-        for include_path, include_key in include_files.items():
-            if filepath.match(include_path):
-                new_changed_files.append(Path(include_key))
-    return new_changed_files
-
-
-def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
-    """
-    Detects and returns a list of nf-test files from the given list of changed files.
-
-    Args:
-        changed_files (list[Path]): A list of file paths.
-
-    Returns:
-        list[Path]: A list of nf-test file paths.
-    """
-    result: list[Path] = []
-    for path in changed_files:
-        # If Path is the exact nf-test file add to list:
-        if path.match("*.nf.test") and path.exists():
-            result.append(path)
-        # Else recursively search for nf-test files:
-        else:
-            # Get the enclosing dir so files in the same dir can be found.
-            # e.g.
-            # dir/
-            # ├─ main.nf
-            # ├─ main.nf.test
-            for file in path.parent.rglob("*.nf.test"):
-                result.append(file)
-    return result
-
-
-def process_files(files: list[Path]) -> list[str]:
-    """
-    Process the files and return lines that begin with 'workflow', 'process', or 'function' and have a single string afterwards.
-
-    Args:
-        files (list): List of files to process.
-
-    Returns:
-        list: List of lines that match the criteria.
-    """
-    result = []
-    for file in files:
-        with open(file, "r") as f:
-            is_pipeline_test = True
-            lines = f.readlines()
-            for line in lines:
-                line = line.strip()
-                if line.startswith(("workflow", "process", "function")):
-                    words = line.split()
-                    if len(words) == 2 and re.match(r'^".*"$', words[1]):
-                        result.append(line)
-                        is_pipeline_test = False
-
-            # If no results included workflow, process or function
-            # Add a dummy result to fill the 'pipeline' category
-            if is_pipeline_test:
-                result.append("pipeline 'PIPELINE'")
-
-    return result
-
-
-def convert_nf_test_files_to_test_types(
-    lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
-) -> dict[str, list[str]]:
-    """
-    Generate a dictionary of function, process and workflow lists from the lines.
-
-    Args:
-        lines (list): List of lines to process.
-        types (list): List of types to include.
-
-    Returns:
-        dict: Dictionary with function, process and workflow lists.
-    """
-    # Populate empty dict from types
-    result: dict[str, list[str]] = {key: [] for key in types}
-
-    for line in lines:
-        words = line.split()
-        if len(words) == 2 and re.match(r'^".*"$', words[1]):
-            keyword = words[0]
-            name = words[1].strip("'\"")  # Strip both single and double quotes
-            if keyword in types:
-                result[keyword].append(name)
-    return result
-
-
-def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
-    """
-    Find all *.nf.test files with changed dependencies from a list of paths.
-
-    Args:
-        paths (list): List of directories or files to scan.
-        tags (list): List of tags identified as having changes.
-
-    Returns:
-        list: List of *.nf.test files with changed dependencies.
-    """
-
-    result: list[Path] = []
-
-    nf_test_files = detect_nf_test_files(paths)
-
-    # find nf-test files with changed dependencies
-    for nf_test_file in nf_test_files:
-        with open(nf_test_file, "r") as f:
-            lines = f.readlines()
-            # Get all tags from nf-test file
-            # Make case insensitive with .casefold()
-            tags_in_nf_test_file = [
-                tag.casefold().replace("/", "_")
-                for tag in convert_nf_test_files_to_test_types(lines, types=["tag"])[
-                    "tag"
-                ]
-            ]
-            # Check if tag in nf-test file appears in a tag.
-            # Use .casefold() to be case insensitive
-            if any(
-                tag.casefold().replace("/", "_") in tags_in_nf_test_file for tag in tags
-            ):
-                result.append(nf_test_file)
-
-    return result
-
-
-if __name__ == "__main__":
-
-    # Utility stuff
-    args = parse_args()
-    logging.basicConfig(level=args.log_level)
-
-    # Parse nf-test files for target test tags
-    changed_files = find_changed_files(args.head_ref, args.base_ref, args.ignored_files)
-
-    # If an additional include YAML is added, we detect additional changed dirs to include
-    if args.include:
-        include_files = read_yaml_inverted(args.include)
-        changed_files = changed_files + detect_include_files(
-            changed_files, include_files
-        )
-    nf_test_files = detect_nf_test_files(changed_files)
-    lines = process_files(nf_test_files)
-    result = convert_nf_test_files_to_test_types(lines)
-
-    # Get only relevant results (specified by -t)
-    # Unique using a set
-    target_results = list(
-        {item for sublist in map(result.get, args.types) for item in sublist}
-    )
-
-    # Parse files to identify nf-tests with changed dependencies
-    changed_dep_files = find_changed_dependencies([Path(".")], target_results)
-
-    # Combine target nf-test files and nf-test files with changed dependencies
-    all_nf_tests = [
-        str(test_path) for test_path in set(changed_dep_files + nf_test_files)
-    ]
-
-    # Print to stdout
-    print(json.dumps(all_nf_tests))
diff --git a/.github/python/include.yaml b/.github/python/include.yaml
deleted file mode 100644
index 6bee890..0000000
--- a/.github/python/include.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-".":
-  - .github/workflows/**
-  - nf-test.config
-  - /./nextflow.config
-tests:
-  - assets/*
-  - bin/*
-  - conf/*
-  - /./main.nf
-  - nextflow_schema.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 46ebe58..b102cc2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,35 +27,23 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Install gitpython find changed files
-        run: |
-          python -m pip install --upgrade pip
-          pip install gitpython pyyaml
-
-      - name: nf-test list nf_test_files
+      - name: List nf-test files
         id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
+
+      - name: print list of nf-test files
         run: |
-          echo nf_test_files=$(python \
-            .github/python/find_changed_files.py \
-            -t pipeline workflow process \
-            --head_ref ${{ github.sha }} \
-            --base_ref origin/${{ github.base_ref }} \
-          ) >> $GITHUB_OUTPUT
-
-      - name: debug
-        run: |
-          echo ${{ steps.list.outputs.nf_test_files }}
+          echo ${{ steps.list.outputs.components }}
 
   test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
@@ -74,10 +62,10 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -106,12 +94,9 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
       - name: Run nf-test
         run: |
-          nf-test test ${{ matrix.nf_test_files }} --verbose --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:
diff --git a/modules.json b/modules.json
index 0fd93f3..99fdeb6 100644
--- a/modules.json
+++ b/modules.json
@@ -59,7 +59,8 @@
                     "genomad/endtoend": {
                         "branch": "master",
                         "git_sha": "9b68cbd01a704aaf2c34f6d6bc7c25e9b4670147",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/genomad/endtoend/genomad-endtoend.diff"
                     },
                     "gunzip": {
                         "branch": "master",
diff --git a/modules/nf-core/genomad/endtoend/environment.yml b/modules/nf-core/genomad/endtoend/environment.yml
new file mode 100644
index 0000000..6ec4ebe
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/environment.yml
@@ -0,0 +1,7 @@
+name: genomad_endtoend
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::genomad=1.7.4
diff --git a/modules/nf-core/genomad/endtoend/genomad-endtoend.diff b/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
index a8b48af..4cf7685 100644
--- a/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
+++ b/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
@@ -1,4 +1,32 @@
 Changes in module 'nf-core/genomad/endtoend'
+--- modules/nf-core/genomad/endtoend/main.nf
++++ modules/nf-core/genomad/endtoend/main.nf
+@@ -2,14 +2,14 @@
+     tag "$meta.id"
+     label 'process_high'
+ 
+-    conda "${moduleDir}/environment.yml"
++    conda "bioconda::genomad=1.5.2"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/genomad:1.7.4--pyhdfd78af_0':
+-        'biocontainers/genomad:1.7.4--pyhdfd78af_0' }"
++        'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
++        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+ 
+     input:
+-    tuple val(meta) , path(fasta)
+-    path  genomad_db
++    tuple val(meta), path(fasta)
++    tuple path(genomad_db)
+ 
+     output:
+     tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification   , optional: true
+@@ -82,4 +82,4 @@
+         genomad: \$(echo \$(genomad --version 2>&1) | sed 's/^.*geNomad, version //; s/ .*\$//')
+     END_VERSIONS
+     """
+-}
++}
 --- /dev/null
 +++ modules/nf-core/genomad/endtoend/nextflow.config
 @@ -0,0 +1,23 @@
@@ -25,65 +53,5 @@ Changes in module 'nf-core/genomad/endtoend'
 +        ]
 +    }
 +}
---- modules/nf-core/genomad/endtoend/main.nf
-+++ modules/nf-core/genomad/endtoend/main.nf
-@@ -8,22 +8,22 @@
-         'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
- 
-     input:
--    tuple val(meta) , path(fasta)
--    path  genomad_db
-+    tuple val(meta), path(fasta)
-+    tuple path(genomad_db)
- 
-     output:
--    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification
-+    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification   , optional: true
-     tuple val(meta), path("*_annotate/*_taxonomy.tsv")                                      , emit: taxonomy
-     tuple val(meta), path("*_find_proviruses/*_provirus.tsv")                               , emit: provirus
-     tuple val(meta), path("*_score_calibration/*_compositions.tsv")                         , emit: compositions                , optional: true
-     tuple val(meta), path("*_score_calibration/*_calibrated_aggregated_classification.tsv") , emit: calibrated_classification   , optional: true
--    tuple val(meta), path("*_summary/*_plasmid.fna")                                        , emit: plasmid_fasta
-+    tuple val(meta), path("*_summary/*_plasmid.fna.gz")                                     , emit: plasmid_fasta
-     tuple val(meta), path("*_summary/*_plasmid_genes.tsv")                                  , emit: plasmid_genes
--    tuple val(meta), path("*_summary/*_plasmid_proteins.faa")                               , emit: plasmid_proteins
-+    tuple val(meta), path("*_summary/*_plasmid_proteins.faa.gz")                            , emit: plasmid_proteins
-     tuple val(meta), path("*_summary/*_plasmid_summary.tsv")                                , emit: plasmid_summary
--    tuple val(meta), path("*_summary/*_virus.fna")                                          , emit: virus_fasta
-+    tuple val(meta), path("*_summary/*_virus.fna.gz")                                       , emit: virus_fasta
-     tuple val(meta), path("*_summary/*_virus_genes.tsv")                                    , emit: virus_genes
--    tuple val(meta), path("*_summary/*_virus_proteins.faa")                                 , emit: virus_proteins
-+    tuple val(meta), path("*_summary/*_virus_proteins.faa.gz")                              , emit: virus_proteins
-     tuple val(meta), path("*_summary/*_virus_summary.tsv")                                  , emit: virus_summary
-     path "versions.yml"                                                                     , emit: versions
- 
-@@ -41,6 +41,9 @@
-         $genomad_db \\
-         --threads $task.cpus \\
-         $args
-+    
-+    gzip ./**/*.fna 
-+    gzip ./**/*.faa
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-@@ -65,13 +68,13 @@
-     touch ${filename}_score_calibration/${filename}_calibrated_aggregated_classification.tsv
-     touch ${filename}_score_calibration/${filename}_compositions.tsv
-     mkdir ${filename}_summary
--    touch ${filename}_summary/${filename}_plasmid.fna
-+    touch ${filename}_summary/${filename}_plasmid.fna.gz
-     touch ${filename}_summary/${filename}_plasmid_genes.tsv
--    touch ${filename}_summary/${filename}_plasmid_proteins.faa
-+    touch ${filename}_summary/${filename}_plasmid_proteins.faa.gz
-     touch ${filename}_summary/${filename}_plasmid_summary.tsv
--    touch ${filename}_summary/${filename}_virus.fna
-+    touch ${filename}_summary/${filename}_virus.fna.gz
-     touch ${filename}_summary/${filename}_virus_genes.tsv
--    touch ${filename}_summary/${filename}_virus_proteins.faa
-+    touch ${filename}_summary/${filename}_virus_proteins.faa.gz
-     touch ${filename}_summary/${filename}_virus_summary.tsv
- 
-     cat <<-END_VERSIONS > versions.yml
 
 ************************************************************
diff --git a/modules/nf-core/genomad/endtoend/main.nf b/modules/nf-core/genomad/endtoend/main.nf
index 5a1937a..0630208 100644
--- a/modules/nf-core/genomad/endtoend/main.nf
+++ b/modules/nf-core/genomad/endtoend/main.nf
@@ -41,8 +41,8 @@ process GENOMAD_ENDTOEND {
         $genomad_db \\
         --threads $task.cpus \\
         $args
-    
-    gzip ./**/*.fna 
+
+    gzip ./**/*.fna
     gzip ./**/*.faa
 
     cat <<-END_VERSIONS > versions.yml
@@ -82,4 +82,4 @@ process GENOMAD_ENDTOEND {
         genomad: \$(echo \$(genomad --version 2>&1) | sed 's/^.*geNomad, version //; s/ .*\$//')
     END_VERSIONS
     """
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/genomad/endtoend/meta.yml b/modules/nf-core/genomad/endtoend/meta.yml
index b5a6f61..044496c 100644
--- a/modules/nf-core/genomad/endtoend/meta.yml
+++ b/modules/nf-core/genomad/endtoend/meta.yml
@@ -1,5 +1,4 @@
 name: "genomad_endtoend"
-
 description: Identify mobile genetic elements present in genomic assemblies
 keywords:
   - metagenomics
@@ -9,7 +8,6 @@ keywords:
   - phage
   - virus
   - plasmid
-
 tools:
   - "genomad":
       description: "Identification of mobile genetic elements"
@@ -17,8 +15,7 @@ tools:
       documentation: https://portal.nersc.gov/genomad/
       tool_dev_url: https://github.com/apcamargo/genomad/
       doi: 10.1101/2023.03.05.531206
-      licence: "['Lawrence Berkeley National Labs BSD variant license']"
-
+      licence: ["Lawrence Berkeley National Labs BSD variant license"]
 input:
   - meta:
       type: map
@@ -35,7 +32,6 @@ input:
   - score_calibration:
       type: boolean
       description: true/false value to indicate if score calibration should be enabled
-
 output:
   - meta:
       type: map
@@ -98,6 +94,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@CarsonJM"
+maintainers:
+  - "@CarsonJM"
diff --git a/modules/nf-core/genomad/endtoend/nextflow.config b/modules/nf-core/genomad/endtoend/nextflow.config
index d108d71..570802a 100644
--- a/modules/nf-core/genomad/endtoend/nextflow.config
+++ b/modules/nf-core/genomad/endtoend/nextflow.config
@@ -20,4 +20,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/genomad/endtoend/tests/main.nf.test b/modules/nf-core/genomad/endtoend/tests/main.nf.test
new file mode 100644
index 0000000..55c6771
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/main.nf.test
@@ -0,0 +1,83 @@
+nextflow_process {
+
+    name "Test Process GENOMAD_ENDTOEND"
+    script "../main.nf"
+    process "GENOMAD_ENDTOEND"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genomad"
+    tag "genomad/download"
+    tag "genomad/endtoend"
+
+    test("sarscov2 - genome - fasta") {
+        setup {
+            run("GENOMAD_DOWNLOAD") {
+                script "../../download/main.nf"
+                }
+            }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                input[1] = GENOMAD_DOWNLOAD.out.genomad_db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.aggregated_classification,
+                    process.out.taxonomy,
+                    process.out.provirus,
+                    process.out.compositions,
+                    process.out.calibrated_classification,
+                    process.out.plasmid_genes,
+                    process.out.virus_fasta,
+                    process.out.virus_genes,
+                    process.out.virus_proteins,
+                    process.out.virus_summary,
+                    process.out.versions,
+                    ).match()
+                },
+                { assert file(process.out.plasmid_fasta.get(0).get(1)).exists() },
+                { assert file(process.out.plasmid_proteins.get(0).get(1)).exists() }
+            )
+        }
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+
+        setup {
+            run("GENOMAD_DOWNLOAD") {
+                script "../../download/main.nf"
+                }
+            }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                input[1] = GENOMAD_DOWNLOAD.out.genomad_db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap b/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap
new file mode 100644
index 0000000..00c02fa
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap
@@ -0,0 +1,281 @@
+{
+    "sarscov2 - genome - fasta": {
+        "content": [
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                ]
+            ],
+            [
+                "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+            ]
+        ],
+        "timestamp": "2024-01-03T00:05:48.225084591"
+    },
+    "sarscov2 - genome - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                    ]
+                ],
+                "13": [
+                    "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_proteins.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_summary.tsv:md5,8c4ddaa8a90da779c11537be0fddb799"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "aggregated_classification": [
+                    
+                ],
+                "calibrated_classification": [
+                    
+                ],
+                "compositions": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                    ]
+                ],
+                "plasmid_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "plasmid_genes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                    ]
+                ],
+                "plasmid_proteins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_proteins.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "plasmid_summary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_summary.tsv:md5,8c4ddaa8a90da779c11537be0fddb799"
+                    ]
+                ],
+                "provirus": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                    ]
+                ],
+                "taxonomy": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+                ],
+                "virus_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "virus_genes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                    ]
+                ],
+                "virus_proteins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                    ]
+                ],
+                "virus_summary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2024-01-03T00:07:52.60021527"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genomad/endtoend/tests/nextflow.config b/modules/nf-core/genomad/endtoend/tests/nextflow.config
new file mode 100644
index 0000000..149f4a4
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GENOMAD_ENDTOEND {
+        ext.args = '--splits 6 --enable-score-calibration --sensitivity 0.1 --disable-nn-classification'
+    }
+}
diff --git a/modules/nf-core/genomad/endtoend/tests/tags.yml b/modules/nf-core/genomad/endtoend/tests/tags.yml
new file mode 100644
index 0000000..497ed72
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/tags.yml
@@ -0,0 +1,2 @@
+genomad/endtoend:
+  - "modules/nf-core/genomad/endtoend/**"