diff --git a/.github/workflows/software/samtools_idxstats.yml b/.github/workflows/software/samtools_idxstats.yml
index a3e64998..efc67e32 100644
--- a/.github/workflows/software/samtools_idxstats.yml
+++ b/.github/workflows/software/samtools_idxstats.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/samtools/idxstats/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_idxstats --symlink --wt 2
diff --git a/.github/workflows/software/samtools_index.yml b/.github/workflows/software/samtools_index.yml
index 57ef33aa..2a1ed2d5 100644
--- a/.github/workflows/software/samtools_index.yml
+++ b/.github/workflows/software/samtools_index.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/samtools/index/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_index --symlink --wt 2
diff --git a/.github/workflows/software/samtools_sort.yml b/.github/workflows/software/samtools_sort.yml
index 02affa2c..a090fcdf 100644
--- a/.github/workflows/software/samtools_sort.yml
+++ b/.github/workflows/software/samtools_sort.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/samtools/sort/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_sort --symlink --wt 2
diff --git a/.github/workflows/software/samtools_stats.yml b/.github/workflows/software/samtools_stats.yml
index c5765235..cbc9e7b3 100644
--- a/.github/workflows/software/samtools_stats.yml
+++ b/.github/workflows/software/samtools_stats.yml
@@ -17,14 +17,20 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
+      - uses: actions/checkout@v2
 
-    - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          export NXF_VER="20.07.1"
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
 
-    - name: Install Nextflow
-      run: |
-        export NXF_VER="20.07.1"
-        wget -qO- get.nextflow.io | bash
-        sudo mv nextflow /usr/local/bin/
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-    # Test the module
-    - run: nextflow run ./software/samtools/stats/test/ -profile docker
+      # Test the module
+      - run: pytest --tag samtools_stats --symlink --wt 2