Important! Template update for nf-core/tools v4.0.3 #1694
Workflow file for this run
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| name: Run nf-test | |
| on: | |
| pull_request: | |
| release: | |
| types: [published] | |
| 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 }} | |
| NFT_VER: "0.9.5" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| jobs: | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test-changes | |
| - runner=4cpu-linux-x64 | |
| 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@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| fetch-depth: 0 | |
| - name: get number of shards | |
| id: set-shards | |
| uses: ./.github/actions/get-shards | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| # Skip sentieon tests on fork PRs where secrets are not available | |
| SKIP_SENTIEON: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq' }} | |
| # Skip GPU tests on CPU runners | |
| SKIP_GPU: "true" | |
| with: | |
| max_shards: 20 | |
| - name: debug | |
| run: | | |
| echo ${{ steps.set-shards.outputs.shard }} | |
| echo ${{ steps.set-shards.outputs.total_shards }} | |
| nf-test: | |
| name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" | |
| needs: [nf-test-changes] | |
| if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test | |
| - runner=4cpu-linux-x64 | |
| - volume=80gb | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} | |
| profile: [conda, docker, singularity] | |
| isMain: | |
| - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMain: false | |
| profile: "conda" | |
| - isMain: false | |
| profile: "singularity" | |
| NXF_VER: | |
| - "25.10.4" | |
| - "latest-everything" | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} | |
| steps: | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| 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 }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| NXF_VERSION: ${{ matrix.NXF_VER }} | |
| # Skip sentieon tests on fork PRs where secrets are not available, | |
| # and on conda because conda-resolved sentieon + its license-server | |
| # handshake isn't deterministic run-to-run, so classifyStrand can | |
| # flip on a threshold boundary and the summary-table md5 drifts | |
| # vs the docker-captured snapshot. | |
| SKIP_SENTIEON: ${{ (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq') || matrix.profile == 'conda' }} | |
| # Skip GPU tests on CPU runners | |
| SKIP_GPU: "true" | |
| with: | |
| profile: test,${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| - 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 ${{ matrix.shard }}/${{ env.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 | |
| # continue-on-error keeps latest-everything from failing the job, so it never shows up in | |
| # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead; | |
| # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those. | |
| - name: Prepare PR comment fragment | |
| if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} | |
| run: | | |
| mkdir -p pr-comment-fragment | |
| echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md | |
| - name: Upload PR comment fragment | |
| if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} | |
| uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 | |
| with: | |
| name: pr-comment-fragment-${{ strategy.job-index }} | |
| path: pr-comment-fragment/ | |
| confirm-pass: | |
| needs: [nf-test-changes, nf-test] | |
| if: always() | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-confirm-pass | |
| - runner=2cpu-linux-x64 | |
| 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::" | |
| - name: Download PR comment fragments | |
| if: ${{ always() }} | |
| uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 | |
| continue-on-error: true | |
| with: | |
| pattern: pr-comment-fragment-* | |
| path: pr-comment-fragments | |
| merge-multiple: true | |
| # Build a comment for the shared pr-comment.yml poster to publish on the PR. | |
| # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported. | |
| - name: Prepare PR comment | |
| if: ${{ always() }} | |
| env: | |
| PR_NUMBER: ${{ github.event.pull_request.number }} | |
| RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| run: | | |
| mkdir -p pr-comment | |
| echo "$PR_NUMBER" > pr-comment/pr_number.txt | |
| echo "nf-test" > pr-comment/header.txt | |
| if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then | |
| { | |
| echo "## ❌ nf-test failed with latest Nextflow version" | |
| echo "" | |
| echo "> [!NOTE]" | |
| echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure." | |
| echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing." | |
| echo "" | |
| cat pr-comment-fragments/*.md | |
| echo "" | |
| echo "See the [full run](${RUN_URL}) for details." | |
| } > pr-comment/comment.md | |
| fi | |
| - name: Upload PR comment artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 | |
| with: | |
| name: pr-comment | |
| path: pr-comment/ |