Greater than 256

.github/workflows/pytest-workflow.yml

@@ -8,18 +8,33 @@ jobs:
     outputs:
       # Expose matched filters as job 'modules' output variable
       modules: ${{ steps.filter.outputs.changes }}
+      proceed: ${{ steps.yq_modules.outputs.proceed }}
     steps:
       - uses: actions/checkout@v2
       - uses: dorny/paths-filter@v2
         id: filter
         with:
           filters: 'tests/config/pytest_software.yml'
 
+      - name: Install yq
+        run: |
+          sudo wget https://github.com/mikefarah/yq/releases/download/v4.6.3/yq_linux_amd64 -O /usr/bin/yq
+          sudo chmod +x /usr/bin/yq
+      # 256 max jobs / 2 nxf versions / 3 profiles
+
+      - name: Fail if number of modules to be tested is greater than 42
+        id: yq_modules
+        run: |
+          output=$(echo ${{ steps.filter.outputs.changes }} | yq e 'length' -)
+          echo "::set-output name=proceed::$(if (test $output -lt 42); then return 0; else return 1; fi)"
+
+
+
   test:
     runs-on: ubuntu-20.04
     name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
     needs: changes
-    if: needs.changes.outputs.modules != '[]'
+    if: needs.changes.outputs.modules != '[]' && needs.changes.outputs.proceed == '0'
     strategy:
       fail-fast: false
       matrix:
@@ -93,3 +108,89 @@ jobs:
             /home/runner/pytest_workflow_*/*/log.out
             /home/runner/pytest_workflow_*/*/log.err
             /home/runner/pytest_workflow_*/*/work
+
+
+  all:
+    runs-on: ubuntu-20.04
+    name: Test all modules
+    needs: changes
+    if: needs.changes.outputs.proceed != '0'
+    strategy:
+      fail-fast: false
+      matrix:
+        nxf_version: ['20.11.0-edge', '21.03.0-edge']
+        profile: ['docker', 'singularity', 'conda']
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - 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
+        # FIXME: Remove this when nf-core modules lint stabilizes
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint . -a
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - 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 Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Setup miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --symlink --kwdof
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-all-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err