fix: biowulf has depreceated SLURM_JOBID in favor of SLURM_JOB_ID #408
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| workflow_dispatch: | |
| inputs: | |
| test_run: | |
| type: boolean | |
| default: false | |
| required: true | |
| env: | |
| test_run: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.test_run }} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 2 | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| mkdir -p tests/bin/ | |
| pip install .[dev,test] | |
| python -c 'from champagne.src.util import chmod_bins_exec; chmod_bins_exec()' | |
| - name: Check CLI basics | |
| run: | | |
| which champagne | |
| champagne --version | |
| champagne --citation | |
| - name: Stub run | |
| run: | | |
| cd tests/cli | |
| champagne init | |
| champagne run -stub -c ci_stub.config --max_cpus 2 --max_memory 6.GB | |
| - name: Test run | |
| if: ${{ env.test_run == 'true' }} | |
| run: | | |
| cd tests/cli | |
| champagne init | |
| champagne run -profile docker -c ci_test.config | |
| - name: "Upload Artifact" | |
| uses: actions/upload-artifact@v3 | |
| if: always() # run even if previous steps fail | |
| with: | |
| name: nextflow-log | |
| path: .nextflow.log | |
| build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871 | |
| runs-on: ubuntu-latest | |
| needs: [build] | |
| if: always() | |
| steps: | |
| - name: Successful build | |
| if: ${{ !(contains(needs.*.result, 'failure')) }} | |
| run: exit 0 | |
| - name: Failing build | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 |