Subworkflow/bam generation

.github/workflows/test.yml

@@ -0,0 +1,236 @@
+name: test
+on:
+  pull_request:
+    branches: [main, develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+
+  pytest-changes:
+    name: pytest-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  nf-core-lint:
+    runs-on: ubuntu-20.04
+    name: nf-core-lint
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        exclude:
+          - tags: "nf-test"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - 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: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        if: ${{ !startsWith(matrix.tags, 'subworkflows/') }}
+
+      - name: Remove substring from matrix.tags
+        id: remove_substring
+        run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT
+
+      - name: Lint subworkflow ${{ matrix.tags }}
+        run: nf-core subworkflows lint ${{ steps.remove_substring.outputs.subworkflow_names }}
+        if: startsWith( matrix.tags, 'subworkflows/' )
+
+  pytest:
+    runs-on: ubuntu-20.04
+    name: pytest
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography GitPython
+
+      - name: Setup Nextflow ${{ matrix.NXF_VER }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up 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 setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@v6
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
+            !${{ github.workspace }}/.singularity
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

.gitignore

@@ -0,0 +1,2 @@
+/modules/nf-core/
+/subworkflows/nf-core/