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
diff --git a/tests/software/bowtie2/test.yml b/tests/software/bowtie2/test.yml
index 85bb01c8..a3c6f31d 100644
--- a/tests/software/bowtie2/test.yml
+++ b/tests/software/bowtie2/test.yml
@@ -47,17 +47,17 @@
     - bowtie2_align
   files:
     - path: output/bowtie2/bowtie2/NC_010473.1.bt2
-      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
     - path: output/bowtie2/bowtie2/NC_010473.2.bt2
-      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
     - path: output/bowtie2/bowtie2/NC_010473.3.bt2
       md5sum: cd201e81724f3099131aec16ef2cc53b
     - path: output/bowtie2/bowtie2/NC_010473.4.bt2
       md5sum: bbb9d6d21ad765d135f95290204e8433
     - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
-      md5sum: 44f719c2fe42e1f35d54e798775846d1
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
     - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
-      md5sum: f3c398bba5158f4039334a932d79c051
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
     - path: output/bowtie2/test.bowtie2.log
       md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
     - path: output/bowtie2/test.bam