CI: add gpu tag test job #8
Workflow file for this run
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| name: Run nf-tests | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # 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: "0.9.2" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VER: "24.10.2" | |
| jobs: | |
| get-shards: | |
| runs-on: ubuntu-latest | |
| name: "Get shards and total number of shards" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | |
| outputs: | |
| shards: ${{ steps.list-shards.outputs.shards }} | |
| total_shards: ${{ steps.list-shards.outputs.total_shards }} | |
| strategy: | |
| fail-fast: true | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: run nf-test-shard action | |
| id: list-shards | |
| uses: ./.github/actions/nf-test-shard | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| nf-test: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| shard: [1, 2] | |
| filter: [pipeline] | |
| profile: [conda, docker_self_hosted, singularity] | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: 2 | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test | |
| 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 }} | |
| shards: ${{ needs.get-shards.outputs.shards }} | |
| total_shards: ${{ needs.get-shards.outputs.total_shards }} | |
| filters: ${{ matrix.filter }} | |
| tags: | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |