bwamem_index fix #288
Workflow file for this run
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| name: Run nf-tests | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "**/meta.yml" | |
| - "**/*.md" | |
| - "**/*.png" | |
| - "**/*.svg" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "ubuntu-latest" | |
| # 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 }} | |
| NFT_VER: "0.9.3" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VER: "24.10.5" | |
| jobs: | |
| get-shards: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-test-get-shards | |
| - runner=2cpu-linux-x64 | |
| name: "Get Shards" | |
| outputs: | |
| shard: ${{ steps.set-shards.outputs.shard }} | |
| total_shards: ${{ steps.set-shards.outputs.total_shards }} | |
| steps: | |
| - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 | |
| with: | |
| fetch-depth: 0 | |
| - name: run nf-test-shard action | |
| id: set-shards | |
| uses: ./.github/actions/nf-test-shard | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| with: | |
| tags: "cpu" | |
| max_shards: 15 | |
| - name: Set outputs | |
| id: set-outputs | |
| run: | | |
| echo "shard=${{ steps.set-shards.outputs.shard }}" >> $GITHUB_ENV | |
| echo "total_shards=${{ steps.set-shards.outputs.total_shards }}" >> $GITHUB_ENV | |
| nf-test: | |
| name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}" | |
| needs: [get-shards] | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| NXF_ANSI_LOG: false | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| # and number of shards is greater than 0 | |
| if: | | |
| needs.get-shards.outputs.total_shards > 0 && | |
| ( | |
| github.event_name != 'push' || | |
| ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' ) | |
| ) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| profile: [conda, docker, singularity] | |
| shard: ${{ fromJson(needs.get-shards.outputs.shard) }} | |
| NXF_VER: | |
| - "25.04.0" | |
| - "latest-everything" | |
| filters: [pipeline] | |
| steps: | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test | |
| id: run_nf_test | |
| uses: ./.github/actions/nf-test | |
| continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} | |
| env: | |
| NFT_WORKDIR: ${{ env.NFT_WORKDIR }} | |
| NXF_VERSION: ${{ matrix.NXF_VER }} | |
| with: | |
| profile: ${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ needs.get-shards.outputs.total_shards }} | |
| filters: ${{ matrix.filters }} | |
| tags: "cpu" | |
| - name: Report test status | |
| if: ${{ always() }} | |
| run: | | |
| if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then | |
| echo "::error::Test with ${{ matrix.NXF_VER }} failed" | |
| # Add to workflow summary | |
| echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ needs.get-shards.outputs.total_shards }}" >> $GITHUB_STEP_SUMMARY | |
| if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then | |
| echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." | |
| fi | |
| if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
| exit 1 | |
| fi | |
| fi | |
| confirm-pass: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-confirm-pass | |
| - runner=2cpu-linux-x64 | |
| needs: [nf-test] | |
| if: always() | |
| steps: | |
| - name: One or more tests failed (excluding latest-everything) | |
| 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-print | |
| if: always() | |
| run: | | |
| echo "::group::DEBUG: `needs` Contents" | |
| echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | |
| echo "::endgroup::" |