fix(trimgalore): clean stale outputs on same-workdir retry #18609
Workflow file for this run
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| name: Run GPU nf-tests | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| paths-ignore: | |
| - "**/meta.yml" | |
| pull_request: | |
| branches: [master] | |
| paths-ignore: | |
| - "**/meta.yml" | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| 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 }} | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFT_VER: "0.9.5" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VER: "25.10.4" | |
| jobs: | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-test-changes-gpu | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| outputs: | |
| # gpu tag outputs | |
| gpu_paths: ${{ steps.list-gpu.outputs.components }} | |
| gpu_shard: ${{ steps.shards-gpu.outputs.shard }} | |
| gpu_total_shards: ${{ steps.shards-gpu.outputs.total_shards }} | |
| # gpu_highmem tag outputs | |
| gpu_highmem_paths: ${{ steps.list-gpu-highmem.outputs.components }} | |
| gpu_highmem_shard: ${{ steps.shards-gpu-highmem.outputs.shard }} | |
| gpu_highmem_total_shards: ${{ steps.shards-gpu-highmem.outputs.total_shards }} | |
| steps: | |
| - name: Clean Workspace | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| fetch-depth: 0 | |
| # Detect gpu and gpu_highmem tests separately | |
| - name: List gpu test files | |
| id: list-gpu | |
| uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6 | |
| with: | |
| head: ${{ github.sha }} | |
| base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha || 'origin/master' }} | |
| n_parents: 0 | |
| tags: "gpu" | |
| - name: List gpu_highmem test files | |
| id: list-gpu-highmem | |
| uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6 | |
| with: | |
| head: ${{ github.sha }} | |
| base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha || 'origin/master' }} | |
| n_parents: 0 | |
| tags: "gpu_highmem" | |
| # Shard each tag independently | |
| - name: Get gpu shards | |
| id: shards-gpu | |
| if: ${{ steps.list-gpu.outputs.components != '[]' }} | |
| uses: ./.github/actions/get-shards | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| with: | |
| max_shards: 2 | |
| paths: "${{ join(fromJson(steps.list-gpu.outputs.components), ' ') }}" | |
| tags: "gpu" | |
| - name: Get gpu_highmem shards | |
| id: shards-gpu-highmem | |
| if: ${{ steps.list-gpu-highmem.outputs.components != '[]' }} | |
| uses: ./.github/actions/get-shards | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| with: | |
| max_shards: 2 | |
| paths: "${{ join(fromJson(steps.list-gpu-highmem.outputs.components), ' ') }}" | |
| tags: "gpu_highmem" | |
| # Standard GPU tests (g4dn.xlarge - 4 vCPU, 16 GB RAM, T4 GPU) | |
| # Runs tests tagged "gpu" (20+ modules: parabricks, amulety, cellpose, etc.) | |
| nf-test-gpu: | |
| runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64" | |
| name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
| needs: [nf-test-changes] | |
| if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes.outputs.gpu_shard) }} | |
| profile: [docker, singularity] | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.gpu_total_shards }} | |
| steps: | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| fetch-depth: 0 | |
| - name: test cuda | |
| run: | | |
| nvidia-smi -L | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| env: | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| with: | |
| profile: ${{ matrix.profile }},gpu | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| paths: "${{ join(fromJson(needs.nf-test-changes.outputs.gpu_paths), ' ') }}" | |
| tags: gpu | |
| # High-memory GPU tests (g4dn.2xlarge - 8 vCPU, 32 GB RAM, T4 GPU) | |
| # Runs tests tagged "gpu_highmem" (currently only parabricks/rnafq2bam, | |
| # which requires >16 GB system RAM) | |
| nf-test-gpu-highmem: | |
| runs-on: "runs-on=${{ github.run_id }}/family=g4dn.2xlarge/image=ubuntu24-gpu-x64" | |
| name: "GPU Test | g4dn.2xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
| needs: [nf-test-changes] | |
| if: ${{ needs.nf-test-changes.outputs.gpu_highmem_total_shards != '0' && needs.nf-test-changes.outputs.gpu_highmem_total_shards != '' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes.outputs.gpu_highmem_shard) }} | |
| profile: [docker, singularity] | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.gpu_highmem_total_shards }} | |
| steps: | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| fetch-depth: 0 | |
| - name: test cuda | |
| run: | | |
| nvidia-smi -L | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| env: | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| with: | |
| profile: ${{ matrix.profile }},gpu | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| paths: "${{ join(fromJson(needs.nf-test-changes.outputs.gpu_highmem_paths), ' ') }}" | |
| tags: gpu_highmem | |
| confirm-pass-gpu: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-confirm-pass-gpu | |
| - runner=2cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| needs: [nf-test-gpu, nf-test-gpu-highmem] | |
| 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') || (needs.nf-test-gpu.result == 'skipped' && needs.nf-test-gpu-highmem.result == 'skipped') }} | |
| run: exit 0 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |