DeepRVAT Pipeline tests 🧬🧪💻🧑🔬 #17
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| name: DeepRVAT Pipeline tests | |
| run-name: DeepRVAT Pipeline tests 🧬🧪💻🧑🔬 | |
| on: [ push ] | |
| jobs: | |
| Smoke-RunTraining: | |
| 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: | |
| 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 ./example \ | |
| --snakefile ./pipelines/run_training.snakefile --show-failed-logs -F |