With steps #10
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| name: DeepRVAT Pipeline tests | ||
| run-name: DeepRVAT Pipeline tests 🧬🧪💻🧑🔬 | ||
| on: [ push ] | ||
| jobs: | ||
| Smoke-RunTraining: | ||
| steps: | ||
| uses: ./.github/workflows/run-pipeline.yml | ||
| with: | ||
| environment_file: ./deeprvat_env_no_gpu.yml | ||
| name: Smoke-RunTraining | ||
| pipeline_cmd: | | ||
| python -m snakemake -n -j 2 --directory ./example \ | ||
| --snakefile ./pipelines/run_training.snakefile --show-failed-logs | ||
| # Pipeline-Tests-RunTraining: | ||
| # runs-on: ubuntu-latest | ||
| # needs: Smoke-RunTraining | ||
| # steps: | ||
| # - name: Check out repository code | ||
| # uses: actions/checkout@v4 | ||
| # - uses: mamba-org/[email protected] | ||
| # with: | ||
| # environment-name: deeprvat-gh-action | ||
| # environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml | ||
| # cache-environment: true | ||
| # cache-downloads: true | ||
| # - name: Install DeepRVAT | ||
| # run: pip install -e ${{ github.workspace }} | ||
| # shell: micromamba-shell {0} | ||
| # # There are no GPUs on the gh worker, so we disable it in the config | ||
| # - name: Update config to use no gpus | ||
| # run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/example/config.yaml" | ||
| # shell: bash -el {0} | ||
| # - name: Run run_training pipeline | ||
| # run: | | ||
| # python -m snakemake -j 2 --directory ${{ github.workspace }}/example \ | ||
| # --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs -F | ||
| # shell: micromamba-shell {0} | ||
