test whole pipeline #12
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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: | ||
| needs: Smoke-RunTraining | ||
| steps: | ||
| uses: ./.github/workflows/run-pipeline.yml | ||
| with: | ||
| environment_file: ./deeprvat_env_no_gpu.yml | ||
| name: Run run_training pipeline | ||
| # There are no GPUs on the gh worker, so we disable it in the config | ||
| prerun_cmd: "sed -i 's/gpus: 1/gpus: 0/' ./example/config.yaml" | ||
| pipeline_cmd: | | ||
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example \ | ||
| --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs -F | ||
