fix: Enhance RSEM output exports and remove unnecessary star_rsem check #154
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| name: Run nf-test on ARM | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "**/meta.yml" | |
| - "**/*.md" | |
| - "**/*.png" | |
| - "**/*.svg" | |
| 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: "0.9.3" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| jobs: | |
| nf-test-changes-arm: | |
| name: nf-test-changes-arm | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test-changes-arm | |
| - runner=4cpu-linux-arm64 | |
| 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: get number of shards | |
| id: set-shards | |
| uses: ./.github/actions/get-shards | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| # Skip sentieon tests - no ARM containers available | |
| SKIP_SENTIEON: true | |
| with: | |
| max_shards: 14 | |
| - name: debug | |
| run: | | |
| echo ${{ steps.set-shards.outputs.shard }} | |
| echo ${{ steps.set-shards.outputs.total_shards }} | |
| nf-test-arm: | |
| name: "${{ matrix.profile }}-${{ matrix.archProfile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes-arm.outputs.total_shards }}" | |
| needs: [nf-test-changes-arm] | |
| if: ${{ needs.nf-test-changes-arm.outputs.total_shards != '0' }} | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test | |
| - runner=4cpu-linux-arm64 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes-arm.outputs.shard) }} | |
| archProfile: [arm64] | |
| profile: [docker] | |
| 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: | |
| - "25.04.0" | |
| - "latest-everything" | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: ${{ needs.nf-test-changes-arm.outputs.total_shards }} | |
| 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 }} | |
| # Skip sentieon tests - no ARM containers available | |
| SKIP_SENTIEON: true | |
| with: | |
| profile: ${{ matrix.profile }},${{ matrix.archProfile }} | |
| 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.archProfile }} | ${{ 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 [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
| exit 1 | |
| fi | |
| fi | |
| confirm-pass-arm: | |
| needs: [nf-test-changes-arm, nf-test-arm] | |
| if: always() | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ 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::" |