From c4ca9761f51f9a3d505e573ec777bc53e1a8fe1a Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Fri, 5 Apr 2024 22:50:24 +0000
Subject: [PATCH 01/14] Added ability to parse setup runs in nf-tests

---
 .github/python/find_changed_files.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index c0c6175..7997eeb 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -185,7 +185,7 @@ def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
     return result
 
 
-def process_files(files: list[Path]) -> list[str]:
+def process_nf_test_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.
 
@@ -239,6 +239,13 @@ def convert_nf_test_files_to_test_types(
             name = words[1].strip("'\"")  # Strip both single and double quotes
             if keyword in types:
                 result[keyword].append(name)
+        elif "run" in line:
+            run_words = words[0].strip(')').split('(')
+            if len(run_words) == 2 and re.match(r'^".*"$', run_words[1]):
+                keyword = run_words[0]
+                name = run_words[1].strip("'\"")  # Strip both single and double quotes
+                if keyword in types:
+                    result[keyword].append(name)
     return result
 
 
@@ -266,8 +273,8 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
             # 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"
+                for tag in convert_nf_test_files_to_test_types(lines, types=["run"])[
+                    "run"
                 ]
             ]
             # Check if tag in nf-test file appears in a tag.
@@ -296,7 +303,7 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
             changed_files, include_files
         )
     nf_test_files = detect_nf_test_files(changed_files)
-    lines = process_files(nf_test_files)
+    lines = process_nf_test_files(nf_test_files)
     result = convert_nf_test_files_to_test_types(lines)
 
     # Get only relevant results (specified by -t)

From 72366a2678872150022597d35861c8b23b78aaab Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Fri, 5 Apr 2024 22:52:32 +0000
Subject: [PATCH 02/14] Test changes

---
 modules/local/viromeqc/install/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/viromeqc/install/main.nf b/modules/local/viromeqc/install/main.nf
index 7e682a2..a49dadb 100644
--- a/modules/local/viromeqc/install/main.nf
+++ b/modules/local/viromeqc/install/main.nf
@@ -1,6 +1,7 @@
 process VIROMEQC_INSTALL {
     label 'process_low'
 
+
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-b28a1a551d380ce8d57f9d83894ccb9559b44404:08a4cf815fcef0080ede5b3633202cbda8edf59b-0':

From a0b657d544e97cc7f4524e378e8365deba98e1d6 Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Mon, 8 Apr 2024 16:21:08 +0000
Subject: [PATCH 03/14] Automatically find nf-files with changed dependencies
 via include statements

---
 .github/python/find_changed_files.py | 73 ++++++++++++++++++++++++----
 1 file changed, 63 insertions(+), 10 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 7997eeb..4e91751 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -158,12 +158,13 @@ def detect_include_files(
     return new_changed_files
 
 
-def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
+def detect_files(changed_files: list[Path], suffix: str) -> 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.
+        suffix (str): File suffix to detect
 
     Returns:
         list[Path]: A list of nf-test file paths.
@@ -171,7 +172,7 @@ def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
     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():
+        if path.match(suffix) and path.exists():
             result.append(path)
         # Else recursively search for nf-test files:
         else:
@@ -180,7 +181,7 @@ def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
             # dir/
             # ├─ main.nf
             # ├─ main.nf.test
-            for file in path.parent.rglob("*.nf.test"):
+            for file in path.parent.rglob(suffix):
                 result.append(file)
     return result
 
@@ -246,12 +247,19 @@ def convert_nf_test_files_to_test_types(
                 name = run_words[1].strip("'\"")  # Strip both single and double quotes
                 if keyword in types:
                     result[keyword].append(name)
+        elif "include {" in line and "include" in types:
+            keyword = words[0]
+            name = words[2].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]:
+def find_nf_tests_with_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
     """
-    Find all *.nf.test files with changed dependencies from a list of paths.
+    Find all *.nf.test files with changed dependencies
+    (identified as modules loaded in the via setup { run("<tool>") } from a list of paths.
 
     Args:
         paths (list): List of directories or files to scan.
@@ -263,7 +271,7 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
 
     result: list[Path] = []
 
-    nf_test_files = detect_nf_test_files(paths)
+    nf_test_files = detect_files(paths, "*.nf.test")
 
     # find nf-test files with changed dependencies
     for nf_test_file in nf_test_files:
@@ -287,6 +295,48 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
     return result
 
 
+def find_nf_files_with_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
+    """
+    Find all *.nf.test files with where the *.nf file uses changed dependencies
+    (identified via include { <tool> }) in *.nf files 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 from *.nf files with changed dependencies.
+    """
+
+    nf_files_w_changed_dependencies: list[Path] = []
+
+    nf_files = detect_files(paths, "*.nf")
+
+    # find nf files with changed dependencies
+    for nf_file in nf_files:
+        with open(nf_file, "r") as f:
+            lines = f.readlines()
+            # Get all include statements from nf file
+            # Make case insensitive with .casefold()
+            includes_in_nf_file = [
+                tag.casefold().replace("/", "_")
+                for tag in convert_nf_test_files_to_test_types(lines, types=["include"])[
+                    "include"
+                ]
+            ]
+            # Check if include in nf file appears in a tag.
+            # Use .casefold() to be case insensitive
+            if any(
+                tag.casefold().replace("/", "_") in includes_in_nf_file for tag in tags
+            ):
+                nf_files_w_changed_dependencies.append(nf_file)
+
+    # find nf-test for nf files with changed dependencies
+    nf_test_files_for_changed_dependencies = detect_files(nf_files_w_changed_dependencies, "*.nf.test")
+
+    return nf_test_files_for_changed_dependencies
+
+
 if __name__ == "__main__":
 
     # Utility stuff
@@ -302,7 +352,7 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
         changed_files = changed_files + detect_include_files(
             changed_files, include_files
         )
-    nf_test_files = detect_nf_test_files(changed_files)
+    nf_test_files = detect_files(changed_files, "*.nf.test")
     lines = process_nf_test_files(nf_test_files)
     result = convert_nf_test_files_to_test_types(lines)
 
@@ -312,12 +362,15 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
         {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)
+    # Parse nf-test files to identify nf-tests containing "setup" with changed module/subworkflow/workflow
+    nf_test_changed_setup = find_nf_tests_with_changed_dependencies([Path(".")], target_results)
+
+    # Parse *.nf files to identify nf-files containing include with changed module/subworkflow/workflow
+    nf_files_changed_include = find_nf_files_with_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)
+        str(test_path) for test_path in set(nf_test_files + nf_test_changed_setup + nf_files_changed_include)
     ]
 
     # Print to stdout

From c64be70b14112659cc3ae4bd478bde6263024b4f Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Mon, 8 Apr 2024 21:38:28 +0000
Subject: [PATCH 04/14] Extra line to test changes

---
 modules/nf-core/mash/sketch/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf
index 77e3d4b..aee3af0 100644
--- a/modules/nf-core/mash/sketch/main.nf
+++ b/modules/nf-core/mash/sketch/main.nf
@@ -6,6 +6,7 @@ process MASH_SKETCH {
         'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
         'biocontainers/mash:2.3--he348c14_1' }"
 
+
     input:
     tuple val(meta), path(reads)
 

From 46f9b5c10c258b091f6bfe874b9f1f0e2f59b9f4 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 16 Apr 2024 17:11:40 +0000
Subject: [PATCH 05/14] Updated workflow to use Adam's GH action

---
 .github/workflows/ci.yml | 72 +++++++++++++++++++++++++---------------
 1 file changed, 46 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 46ebe58..0cb57e9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,44 +23,44 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  changes:
-    name: Check for changes
+  nf-test-changes:
+    name: nf-test-changes
     runs-on: ubuntu-latest
     outputs:
-      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
-    steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
+      # Expose detected tags as 'modules' and 'workflows' output variables
+      paths: ${{ steps.list.outputs.components }}
+      modules: ${{ steps.outputs.outputs.modules }}
+      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
+      # Prod for version bumping
 
-      - uses: actions/checkout@v3
+    steps:
+      - uses: actions/checkout@v4
         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@main
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          n_parents: 2
+
+      - name: Separate modules and subworkflows
+        id: outputs
         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 }} \
-          ) >> $GITHUB_OUTPUT
+          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT
 
       - name: debug
         run: |
-          echo ${{ steps.list.outputs.nf_test_files }}
+          echo ${{ steps.outputs.outputs.modules }}
+          echo ${{ steps.outputs.outputs.subworkflows }}
 
-  test:
+  nf-test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
-    needs: [changes]
-    if: needs.changes.outputs.nf_test_files != '[]'
+    needs: [nf-test-changes]
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -110,8 +110,23 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run nf-test
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
-          nf-test test ${{ matrix.nf_test_files }} --verbose --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
+          if [ "${{ matrix.profile }}" == "docker" ]; then
+            PROFILE="docker_self_hosted"
+          else
+            PROFILE=${{ matrix.profile }}
+          fi
+
+          NFT_WORKDIR=~ \
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tap=test.tap \
+            --verbose \
+            ${{ matrix.path }}
 
       - uses: pcolby/tap-summary@v1
         with:
@@ -130,6 +145,11 @@ jobs:
         with:
           report_paths: test.xml
 
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/
+
   confirm-pass:
     runs-on: ubuntu-latest
     needs:

From bf86cce3a04bfb265f0ee0d1b8da75dc3526a169 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 16 Apr 2024 18:58:37 +0000
Subject: [PATCH 06/14] Trying to run CI workflow

---
 .github/workflows/ci.yml | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0cb57e9..51daf48 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -59,25 +59,21 @@ jobs:
 
   nf-test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    runs-on: ubuntu-latest
     needs: [nf-test-changes]
     if: ( needs.nf-test-changes.outputs.paths != '[]' )
-    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "latest-everything"
-          - "23.04"
-        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
-        profile:
-          - "docker"
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [docker]
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -114,13 +110,6 @@ jobs:
           NFT_DIFF: "pdiff"
           NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
-          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
-          if [ "${{ matrix.profile }}" == "docker" ]; then
-            PROFILE="docker_self_hosted"
-          else
-            PROFILE=${{ matrix.profile }}
-          fi
-
           NFT_WORKDIR=~ \
           nf-test test \
             --profile=${{ matrix.profile }} \

From 475325c140864b1675d86bd2b2986003d0e4b4b4 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 16 Apr 2024 19:08:46 +0000
Subject: [PATCH 07/14] Tried getting CI workflow to run again

---
 .github/workflows/ci.yml | 44 ++++++++++------------------------------
 1 file changed, 11 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 51daf48..6a49d0a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,20 +10,18 @@ on:
     branches:
       - master
       - dev
-
 env:
   NXF_ANSI_LOG: false
   NFT_VER: "0.8.4"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
-
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  nf-test-changes:
+  changes:
     name: nf-test-changes
     runs-on: ubuntu-latest
     outputs:
@@ -31,8 +29,6 @@ jobs:
       paths: ${{ steps.list.outputs.components }}
       modules: ${{ steps.outputs.outputs.modules }}
       subworkflows: ${{ steps.outputs.outputs.subworkflows}}
-      # Prod for version bumping
-
     steps:
       - uses: actions/checkout@v4
         with:
@@ -57,36 +53,37 @@ jobs:
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
 
-  nf-test:
+  test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
-    runs-on: ubuntu-latest
     needs: [nf-test-changes]
     if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
-        profile: [docker]
+        NXF_VER:
+          - "latest-everything"
+          - "23.04"
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
+        profile:
+          - "docker"
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
-
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
           architecture: "x64"
-
       - name: Install pdiff to see diff between nf-test snapshots
         run: |
           python -m pip install --upgrade pip
           pip install pdiff
-
       - name: Cache nf-test installation
         id: cache-software
         uses: actions/cache@v3
@@ -95,50 +92,32 @@ jobs:
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
           key: ${{ runner.os }}-${{ env.NFT_VER }}-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: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run nf-test
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
-          NFT_WORKDIR=~ \
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tap=test.tap \
-            --verbose \
-            ${{ matrix.path }}
-
+          nf-test test ${{ matrix.nf_test_files }} --verbose --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
       - uses: pcolby/tap-summary@v1
         with:
           path: >-
             test.tap
-
       - name: Output log on failure
         if: failure()
         run: |
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
-
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
 
-      - name: Clean up
-        if: always()
-        run: |
-          sudo rm -rf /home/ubuntu/tests/
-
   confirm-pass:
     runs-on: ubuntu-latest
     needs:
@@ -152,7 +131,6 @@ jobs:
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
-
       - name: debug-print
         if: always()
         run: |

From 05e6e8937df5c772a9d61e4fbcbedc1fce1ca5ac Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 16 Apr 2024 19:30:55 +0000
Subject: [PATCH 08/14] Changed step names to try and run CI action

---
 .github/python/find_changed_files.py | 377 ---------------------------
 .github/python/include.yaml          |  10 -
 .github/workflows/ci.yml             |  16 +-
 3 files changed, 9 insertions(+), 394 deletions(-)
 delete mode 100644 .github/python/find_changed_files.py
 delete mode 100644 .github/python/include.yaml

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
deleted file mode 100644
index 4e91751..0000000
--- a/.github/python/find_changed_files.py
+++ /dev/null
@@ -1,377 +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_files(changed_files: list[Path], suffix: str) -> 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.
-        suffix (str): File suffix to detect
-
-    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(suffix) 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(suffix):
-                result.append(file)
-    return result
-
-
-def process_nf_test_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)
-        elif "run" in line:
-            run_words = words[0].strip(')').split('(')
-            if len(run_words) == 2 and re.match(r'^".*"$', run_words[1]):
-                keyword = run_words[0]
-                name = run_words[1].strip("'\"")  # Strip both single and double quotes
-                if keyword in types:
-                    result[keyword].append(name)
-        elif "include {" in line and "include" in types:
-            keyword = words[0]
-            name = words[2].strip("'\"")  # Strip both single and double quotes
-            if keyword in types:
-                result[keyword].append(name)
-
-    return result
-
-
-def find_nf_tests_with_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
-    """
-    Find all *.nf.test files with changed dependencies
-    (identified as modules loaded in the via setup { run("<tool>") } 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_files(paths, "*.nf.test")
-
-    # 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=["run"])[
-                    "run"
-                ]
-            ]
-            # 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
-
-
-def find_nf_files_with_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
-    """
-    Find all *.nf.test files with where the *.nf file uses changed dependencies
-    (identified via include { <tool> }) in *.nf files 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 from *.nf files with changed dependencies.
-    """
-
-    nf_files_w_changed_dependencies: list[Path] = []
-
-    nf_files = detect_files(paths, "*.nf")
-
-    # find nf files with changed dependencies
-    for nf_file in nf_files:
-        with open(nf_file, "r") as f:
-            lines = f.readlines()
-            # Get all include statements from nf file
-            # Make case insensitive with .casefold()
-            includes_in_nf_file = [
-                tag.casefold().replace("/", "_")
-                for tag in convert_nf_test_files_to_test_types(lines, types=["include"])[
-                    "include"
-                ]
-            ]
-            # Check if include in nf file appears in a tag.
-            # Use .casefold() to be case insensitive
-            if any(
-                tag.casefold().replace("/", "_") in includes_in_nf_file for tag in tags
-            ):
-                nf_files_w_changed_dependencies.append(nf_file)
-
-    # find nf-test for nf files with changed dependencies
-    nf_test_files_for_changed_dependencies = detect_files(nf_files_w_changed_dependencies, "*.nf.test")
-
-    return nf_test_files_for_changed_dependencies
-
-
-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_files(changed_files, "*.nf.test")
-    lines = process_nf_test_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 nf-test files to identify nf-tests containing "setup" with changed module/subworkflow/workflow
-    nf_test_changed_setup = find_nf_tests_with_changed_dependencies([Path(".")], target_results)
-
-    # Parse *.nf files to identify nf-files containing include with changed module/subworkflow/workflow
-    nf_files_changed_include = find_nf_files_with_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(nf_test_files + nf_test_changed_setup + nf_files_changed_include)
-    ]
-
-    # 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 6a49d0a..8f29934 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,7 +21,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  changes:
+  nf-test-changes:
     name: nf-test-changes
     runs-on: ubuntu-latest
     outputs:
@@ -53,8 +53,8 @@ jobs:
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
 
-  test:
-    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+  nf-test:
+    name: nf-test
     needs: [nf-test-changes]
     if: ( needs.nf-test-changes.outputs.paths != '[]' )
     runs-on: ubuntu-latest
@@ -102,7 +102,11 @@ jobs:
 
       - 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 ${{ matrix.nf_test_files }} \
+          --verbose \
+          --profile "+${{ matrix.profile }}" -\
+          -junitxml=test.xml \
+          --tap=test.tap
       - uses: pcolby/tap-summary@v1
         with:
           path: >-
@@ -120,9 +124,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs:
-      - changes
-      - test
+    needs: [nf-test-changes, nf-test]
     if: always()
     steps:
       - name: All tests ok

From 9682de7a9c08afb8ac409383d4e237d1881f3809 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 16 Apr 2024 19:38:41 +0000
Subject: [PATCH 09/14] Changed source of nf-test files

---
 .github/workflows/ci.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8f29934..0830d53 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,10 +61,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
         NXF_VER:
           - "latest-everything"
           - "23.04"
-        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
@@ -101,12 +101,16 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run nf-test
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
-          nf-test test ${{ matrix.nf_test_files }} \
-          --verbose \
-          --profile "+${{ matrix.profile }}" -\
-          -junitxml=test.xml \
-          --tap=test.tap
+          NFT_WORKDIR=~ \
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tap=test.tap \
+            --verbose \
+            ${{ matrix.path }}
       - uses: pcolby/tap-summary@v1
         with:
           path: >-

From 75eae223f4a9a0e6c5e469fd28d10712693542e1 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 23 Apr 2024 16:08:08 +0000
Subject: [PATCH 10/14] Updated CI to match nf-core/fetchngs

---
 .github/workflows/ci.yml | 66 ++++++++++++++++++----------------------
 1 file changed, 29 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0830d53..4c535bd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,80 +10,75 @@ on:
     branches:
       - master
       - dev
+
 env:
   NXF_ANSI_LOG: false
   NFT_VER: "0.8.4"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  nf-test-changes:
-    name: nf-test-changes
+  changes:
+    name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      # Expose detected tags as 'modules' and 'workflows' output variables
-      paths: ${{ steps.list.outputs.components }}
-      modules: ${{ steps.outputs.outputs.modules }}
-      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@main
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.1
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}
-          n_parents: 2
-
-      - name: Separate modules and subworkflows
-        id: outputs
-        run: |
-          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT
-          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT
+          include: .github/include.yaml
 
-      - name: debug
+      - name: print list of nf-test files
         run: |
-          echo ${{ steps.outputs.outputs.modules }}
-          echo ${{ steps.outputs.outputs.subworkflows }}
+          echo ${{ steps.list.outputs.components }}
 
-  nf-test:
-    name: nf-test
-    needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+  test:
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    needs: [changes]
+    if: needs.changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
         NXF_VER:
           - "latest-everything"
           - "23.04"
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
     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 }}"
+
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
           architecture: "x64"
+
       - name: Install pdiff to see diff between nf-test snapshots
         run: |
           python -m pip install --upgrade pip
           pip install pdiff
+
       - name: Cache nf-test installation
         id: cache-software
         uses: actions/cache@v3
@@ -92,34 +87,28 @@ jobs:
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
           key: ${{ runner.os }}-${{ env.NFT_VER }}-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: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run nf-test
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
-          NFT_WORKDIR=~ \
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tap=test.tap \
-            --verbose \
-            ${{ matrix.path }}
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
       - uses: pcolby/tap-summary@v1
         with:
           path: >-
             test.tap
+
       - name: Output log on failure
         if: failure()
         run: |
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
         if: always() # always run even if the previous step fails
@@ -128,7 +117,9 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [nf-test-changes, nf-test]
+    needs:
+      - changes
+      - test
     if: always()
     steps:
       - name: All tests ok
@@ -137,6 +128,7 @@ jobs:
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
+
       - name: debug-print
         if: always()
         run: |

From b20f4c9262d3ce4f54fa89bd5066385e80f460d8 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 23 Apr 2024 16:09:59 +0000
Subject: [PATCH 11/14] Added include.yaml

---
 .github/include.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .github/include.yaml

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

From 84ef43025eb9ab78fd478680d0ad820665ba5a8c Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 23 Apr 2024 16:20:52 +0000
Subject: [PATCH 12/14] Updated genomad/endtoend and removed test changes from
 mash/sketch and viromeqc/install

---
 modules/local/viromeqc/install/main.nf        |   1 -
 .../nf-core/genomad/endtoend/environment.yml  |   7 +
 .../genomad/endtoend/genomad-endtoend.diff    |  89 ------
 modules/nf-core/genomad/endtoend/main.nf      |   6 +-
 modules/nf-core/genomad/endtoend/meta.yml     |   9 +-
 .../nf-core/genomad/endtoend/nextflow.config  |   2 +-
 .../genomad/endtoend/tests/main.nf.test       |  83 ++++++
 .../genomad/endtoend/tests/main.nf.test.snap  | 281 ++++++++++++++++++
 .../genomad/endtoend/tests/nextflow.config    |   5 +
 .../nf-core/genomad/endtoend/tests/tags.yml   |   2 +
 modules/nf-core/mash/sketch/main.nf           |   1 -
 11 files changed, 385 insertions(+), 101 deletions(-)
 create mode 100644 modules/nf-core/genomad/endtoend/environment.yml
 delete mode 100644 modules/nf-core/genomad/endtoend/genomad-endtoend.diff
 create mode 100644 modules/nf-core/genomad/endtoend/tests/main.nf.test
 create mode 100644 modules/nf-core/genomad/endtoend/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/genomad/endtoend/tests/nextflow.config
 create mode 100644 modules/nf-core/genomad/endtoend/tests/tags.yml

diff --git a/modules/local/viromeqc/install/main.nf b/modules/local/viromeqc/install/main.nf
index a49dadb..7e682a2 100644
--- a/modules/local/viromeqc/install/main.nf
+++ b/modules/local/viromeqc/install/main.nf
@@ -1,7 +1,6 @@
 process VIROMEQC_INSTALL {
     label 'process_low'
 
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-b28a1a551d380ce8d57f9d83894ccb9559b44404:08a4cf815fcef0080ede5b3633202cbda8edf59b-0':
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
deleted file mode 100644
index a8b48af..0000000
--- a/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
+++ /dev/null
@@ -1,89 +0,0 @@
-Changes in module 'nf-core/genomad/endtoend'
---- /dev/null
-+++ modules/nf-core/genomad/endtoend/nextflow.config
-@@ -0,0 +1,23 @@
-+process {
-+    withName: GENOMAD_ENDTOEND {
-+        ext.args   = [
-+            params.genomad_min_score ? "--min-score ${params.genomad_min_score}" : "",
-+            params.genomad_max_fdr ? "--enable-score-calibration --max-fdr ${params.genomad_max_fdr}" : "",
-+            params.genomad_splits ? "--splits ${params.genomad_splits}" : "",
-+            params.genomad_disable_nn ? "--disable-nn-classification" : "",
-+            params.genomad_sensitivity ? "--sensitivity ${params.genomad_sensitivity}" : ""
-+        ].join(' ').trim()
-+        publishDir = [
-+            [
-+                path: { "${params.outdir}/VirusClassification/genomad/endtoend" },
-+                mode: params.publish_dir_mode,
-+                pattern: '*_summary/*_virus.fna.gz'
-+            ],
-+            [
-+                path: { "${params.outdir}/VirusClassification/genomad/endtoend" },
-+                mode: params.publish_dir_mode,
-+                pattern: '*_summary/*_virus_summary.tsv'
-+            ]
-+        ]
-+    }
-+}
---- 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/**"
diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf
index aee3af0..77e3d4b 100644
--- a/modules/nf-core/mash/sketch/main.nf
+++ b/modules/nf-core/mash/sketch/main.nf
@@ -6,7 +6,6 @@ process MASH_SKETCH {
         'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
         'biocontainers/mash:2.3--he348c14_1' }"
 
-
     input:
     tuple val(meta), path(reads)
 

From 66d082ced68853afa8c0cb1a774b77bde2f34957 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 23 Apr 2024 16:24:13 +0000
Subject: [PATCH 13/14] Added patch to genomad

---
 modules.json                                  |  3 +-
 .../genomad/endtoend/genomad-endtoend.diff    | 57 +++++++++++++++++++
 2 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/genomad/endtoend/genomad-endtoend.diff

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/genomad-endtoend.diff b/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
new file mode 100644
index 0000000..4cf7685
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/genomad-endtoend.diff
@@ -0,0 +1,57 @@
+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 @@
++process {
++    withName: GENOMAD_ENDTOEND {
++        ext.args   = [
++            params.genomad_min_score ? "--min-score ${params.genomad_min_score}" : "",
++            params.genomad_max_fdr ? "--enable-score-calibration --max-fdr ${params.genomad_max_fdr}" : "",
++            params.genomad_splits ? "--splits ${params.genomad_splits}" : "",
++            params.genomad_disable_nn ? "--disable-nn-classification" : "",
++            params.genomad_sensitivity ? "--sensitivity ${params.genomad_sensitivity}" : ""
++        ].join(' ').trim()
++        publishDir = [
++            [
++                path: { "${params.outdir}/VirusClassification/genomad/endtoend" },
++                mode: params.publish_dir_mode,
++                pattern: '*_summary/*_virus.fna.gz'
++            ],
++            [
++                path: { "${params.outdir}/VirusClassification/genomad/endtoend" },
++                mode: params.publish_dir_mode,
++                pattern: '*_summary/*_virus_summary.tsv'
++            ]
++        ]
++    }
++}
+
+************************************************************

From f9da24f4beb5775735a28d98327bd92755517a8a Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Tue, 23 Apr 2024 17:09:51 +0000
Subject: [PATCH 14/14] Updated adam's GH action version

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4c535bd..b102cc2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0.1
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}