diff --git a/.github/workflows/bowtie2_align.yml b/.github/workflows/bowtie2_align.yml
new file mode 100644
index 00000000..3642b5c9
--- /dev/null
+++ b/.github/workflows/bowtie2_align.yml
@@ -0,0 +1,42 @@
+name: bowtie2_align
+on:
+    push:
+        paths:
+            - software/bowtie2/align/**
+            - software/bowtie2/build/**
+            - .github/workflows/bowtie2_align.yml
+            - tests/software/bowtie2/**
+    pull_request:
+        paths:
+            - software/bowtie2/align/**
+            - software/bowtie2/build/**
+            - .github/workflows/bowtie2_align.yml
+            - tests/software/bowtie2/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                nxf_version: [20.11.0-edge]
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              env:
+                  NXF_VER: ${{ matrix.nxf_version }}
+              run: |
+                  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: pytest --tag bowtie2_align --symlink --wt 2
diff --git a/.github/workflows/bowtie2_build.yml b/.github/workflows/bowtie2_build.yml
new file mode 100644
index 00000000..21ddde78
--- /dev/null
+++ b/.github/workflows/bowtie2_build.yml
@@ -0,0 +1,40 @@
+name: bowtie2_build
+on:
+  push:
+    paths:
+      - software/bowtie2/build/**
+      - .github/workflows/bowtie2_build.yml
+      - tests/software/bowtie2/**
+  pull_request:
+    paths:
+      - software/bowtie2/build/**
+      - .github/workflows/bowtie2_build.yml
+      - tests/software/bowtie2/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          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: pytest --tag bowtie2_build --symlink --wt 2