Split functional tests by module, to reduce total runtime

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  test:
+  test-dry-run:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -52,3 +52,51 @@ jobs:
           bash -c '
           for file in $(find /tmp -name log.err);
           do echo $file; cat $file; done'
+
+  test-functional:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        module:
+          - qc
+          - itd
+          - fusion
+          - expression
+          - snv-indels
+          - hamlet
+    steps:
+      - uses: actions/checkout@v2.3.4 # https://github.com/actions/checkout.
+        with:
+          submodules: recursive
+
+      - name: Set up Conda environment
+        uses: conda-incubator/setup-miniconda@v2.0.1 # https://github.com/conda-incubator/setup-miniconda.
+        with:
+          activate-environment: HAMLET
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Install singularity
+        uses: eWaterCycle/setup-singularity@v6
+        with:
+          singularity-version: 3.6.4
+
+      - name: Run test in conda environment
+        run: >-
+          pytest --keep-workflow-wd-on-fail
+          --tag ${{ matrix.module}}
+          --tag functional
+
+      - name: Check pytest stdout messages in case of failure
+        if: ${{ failure() }}
+        run: >-
+          bash -c '
+          for file in $(find /tmp -name log.out);
+          do echo $file; cat $file; done'
+
+      - name: Check pytest stderr messages in case of failure
+        if: ${{ failure() }}
+        run: >-
+          bash -c '
+          for file in $(find /tmp -name log.err);
+          do echo $file; cat $file; done'