minor change #14
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| paths-ignore: | |
| - "**/meta.yml" | |
| pull_request: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - "**/meta.yml" | |
| workflow_dispatch: | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NXF_ANSI_LOG: false | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| NXF_VER: "25.04.8" | |
| jobs: | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install editorconfig-checker | |
| run: pip install editorconfig-checker | |
| - name: Run editorconfig-checker | |
| run: ec | |
| detect-changed-modules: | |
| name: Detect changed modules | |
| runs-on: ubuntu-latest | |
| outputs: | |
| paths: ${{ steps.list.outputs.paths }} | |
| modules: ${{ steps.components.outputs.modules }} | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Detect changed test paths | |
| id: list | |
| run: | | |
| # Get base commit for comparison | |
| if [ "${{ github.event_name }}" == "pull_request" ]; then | |
| BASE_SHA="${{ github.event.pull_request.base.sha }}" | |
| else | |
| BASE_SHA="HEAD~1" | |
| fi | |
| echo "Comparing against: $BASE_SHA" | |
| # Get changed files | |
| CHANGED_FILES=$(git diff --name-only $BASE_SHA...HEAD || git diff --name-only HEAD~1 HEAD) | |
| echo "Changed files:" | |
| echo "$CHANGED_FILES" | |
| # Extract test paths for changed modules | |
| CHANGED_PATHS=() | |
| while IFS= read -r file; do | |
| # Check if file is in modules directory | |
| if [[ "$file" =~ ^modules/([^/]+)/([^/]+)/ ]]; then | |
| org="${BASH_REMATCH[1]}" | |
| module="${BASH_REMATCH[2]}" | |
| test_path="tests/modules/${org}/${module}" | |
| # Check if test exists | |
| if [ -d "$test_path" ]; then | |
| if [[ ! " ${CHANGED_PATHS[@]} " =~ " ${test_path} " ]]; then | |
| CHANGED_PATHS+=("$test_path") | |
| fi | |
| fi | |
| fi | |
| # Also check if test files themselves changed | |
| if [[ "$file" =~ ^tests/modules/([^/]+)/([^/]+)/ ]]; then | |
| test_path="$file" | |
| # Remove the main.nf or nextflow.config to get the directory | |
| test_path="${test_path%/*}" | |
| if [[ ! " ${CHANGED_PATHS[@]} " =~ " ${test_path} " ]]; then | |
| CHANGED_PATHS+=("$test_path") | |
| fi | |
| fi | |
| done <<< "$CHANGED_FILES" | |
| # Convert to JSON array | |
| if [ ${#CHANGED_PATHS[@]} -eq 0 ]; then | |
| echo 'paths=[]' >> $GITHUB_OUTPUT | |
| echo "No changed modules with tests found." | |
| else | |
| PATHS_JSON=$(printf '%s\n' "${CHANGED_PATHS[@]}" | jq -R . | jq -s .) | |
| { | |
| echo "paths<<EOF" | |
| echo "$PATHS_JSON" | |
| echo "EOF" | |
| } >> $GITHUB_OUTPUT | |
| echo "Changed test paths:" | |
| printf '%s\n' "${CHANGED_PATHS[@]}" | |
| fi | |
| - name: Separate modules | |
| id: components | |
| run: | | |
| PATHS='${{ steps.list.outputs.paths }}' | |
| if [ "$PATHS" == "[]" ]; then | |
| echo 'modules=[]' >> $GITHUB_OUTPUT | |
| else | |
| MODULES=$(echo "$PATHS" | jq -c 'map(gsub("tests/modules/"; ""))') | |
| { | |
| echo "modules<<EOF" | |
| echo "$MODULES" | |
| echo "EOF" | |
| } >> $GITHUB_OUTPUT | |
| fi | |
| - name: Debug | |
| run: | | |
| echo "Paths: ${{ steps.list.outputs.paths }}" | |
| echo "Modules: ${{ steps.components.outputs.modules }}" | |
| test-modules: | |
| name: "${{ matrix.profile }} | ${{ matrix.module }}" | |
| needs: [detect-changed-modules] | |
| if: needs.detect-changed-modules.outputs.modules != '[]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJson(needs.detect-changed-modules.outputs.modules) }} | |
| profile: [docker] | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: ${{ env.NXF_VER }} | |
| - name: Run test for ${{ matrix.module }} | |
| run: | | |
| MODULE_PATH="${{ matrix.module }}" | |
| TEST_DIR="tests/modules/${MODULE_PATH}" | |
| echo "Testing module: ${MODULE_PATH}" | |
| echo "Test directory: ${TEST_DIR}" | |
| echo "Profile: ${{ matrix.profile }}" | |
| if [ ! -d "${TEST_DIR}" ]; then | |
| echo "Error: Test directory ${TEST_DIR} not found" | |
| exit 1 | |
| fi | |
| cd "${TEST_DIR}" | |
| # Create output directory | |
| mkdir -p "../../../test_results/${MODULE_PATH}" | |
| # Run test with specified profile | |
| if [ "${{ matrix.profile }}" == "docker" ]; then | |
| PROFILE_FLAG="-with-docker" | |
| elif [ "${{ matrix.profile }}" == "singularity" ]; then | |
| PROFILE_FLAG="-with-singularity" | |
| else | |
| PROFILE_FLAG="" | |
| fi | |
| # Run test workflow | |
| # Nextflow will automatically detect and run the workflow defined in main.nf | |
| nextflow run main.nf \ | |
| -c nextflow.config \ | |
| -c ../../../config/nextflow.config \ | |
| --outdir "../../../test_results/${MODULE_PATH}" \ | |
| $PROFILE_FLAG \ | |
| -with-report "../../../test_results/${MODULE_PATH}/report.html" \ | |
| -with-trace "../../../test_results/${MODULE_PATH}/trace.txt" \ | |
| || exit 1 | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-results-${{ matrix.profile }}-${{ matrix.module }} | |
| path: test_results/${{ matrix.module }}/ | |
| retention-days: 7 | |
| confirm-pass-tests: | |
| name: Confirm all tests passed | |
| runs-on: ubuntu-latest | |
| needs: [test-modules] | |
| if: always() | |
| steps: | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: One or more tests cancelled | |
| if: ${{ contains(needs.*.result, 'cancelled') }} | |
| run: exit 1 | |
| - name: All tests ok | |
| if: ${{ contains(needs.*.result, 'success') }} | |
| run: exit 0 | |
| - name: Debug | |
| if: always() | |
| run: | | |
| echo "::group::DEBUG: Test Results" | |
| echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | |
| echo "::endgroup::" |