DeepRVAT Pipeline Tests 🧬🧪💻🧑🔬 #59
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| name: DeepRVAT Pipeline Tests | |
| run-name: DeepRVAT Pipeline Tests 🧬🧪💻🧑🔬 | |
| on: [ push ] | |
| jobs: | |
| # Training Pipeline | |
| Smoke-RunTraining: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| Pipeline-Tests-RunTraining: | |
| needs: Smoke-RunTraining | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| dry_run: false | |
| # Association Testing Pretrained Pipeline | |
| Smoke-Association-Testing-Pretrained: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && ln -s ../pretrained_models | |
| Pipeline-Tests-Training-Association-Testing: | |
| needs: Smoke-Association-Testing-Pretrained | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && ln -s ../pretrained_models | |
| dry_run: false | |
| # Association Testing Pretrained Regenie | |
| Smoke-Association-Testing-Pretrained-Regenie: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && ln -s ../pretrained_models | |
| Pipeline-Tests-Association-Testing-Pretrained-Regenie: | |
| needs: Smoke-Association-Testing-Pretrained-Regenie | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && ln -s ../pretrained_models | |
| dry_run: false | |
| # Association Testing Training | |
| Smoke-Association-Testing-Training: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/training_association_testing.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| Pipeline-Tests-Association-Testing-Training: | |
| needs: Smoke-Association-Testing-Training | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/training_association_testing.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| dry_run: false | |
| # Association Testing Training Regenie | |
| Smoke-Association-Testing-Training-Regenie: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/training_association_testing_regenie.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| Pipeline-Tests-Training-Association-Testing-Regenie: | |
| needs: Smoke-Association-Testing-Training-Regenie | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/training_association_testing_regenie.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| dry_run: false | |
| # Seed Gene Discovery | |
| Smoke-Seed-Gene-Discovery: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/seed_gene_discovery.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && cp ../deeprvat/seed_gene_discovery/config.yaml . | |
| Pipeline-Tests-Seed-Gene-Discovery: | |
| needs: Smoke-Seed-Gene-Discovery | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/seed_gene_discovery.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cd ./example && cp ../deeprvat/seed_gene_discovery/config.yaml . | |
| dry_run: false | |
| # Preprocessing With QC | |
| Smoke-Preprocessing-With-QC: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/preprocess_with_qc.snakefile | |
| environment_file: ./deeprvat_preprocessing_env.yml | |
| pipeline_directory: ./example/preprocess | |
| pipeline_config: ./pipelines/config/deeprvat_preprocess_config.yaml | |
| download_fasta_data: true | |
| fasta_download_path: ./example/preprocess/workdir/reference | |
| Pipeline-Tests-Preprocessing-With-QC: | |
| needs: Smoke-Preprocessing-With-QC | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/preprocess_with_qc.snakefile | |
| environment_file: ./deeprvat_preprocessing_env.yml | |
| pipeline_directory: ./example/preprocess | |
| pipeline_config: ./pipelines/config/deeprvat_preprocess_config.yaml | |
| dry_run: false | |
| download_fasta_data: true | |
| fasta_download_path: ./example/preprocess/workdir/reference | |
| # Preprocessing-No-QC | |
| Smoke-Preprocessing-No-QC: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/preprocess_no_qc.snakefile | |
| environment_file: ./deeprvat_preprocessing_env.yml | |
| pipeline_directory: ./example/preprocess | |
| pipeline_config: ./pipelines/config/deeprvat_preprocess_config.yaml | |
| download_fasta_data: true | |
| fasta_download_path: ./example/preprocess/workdir/reference | |
| Pipeline-Tests-Preprocessing-No-QC: | |
| needs: Smoke-Preprocessing-No-QC | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/preprocess_no_qc.snakefile | |
| environment_file: ./deeprvat_preprocessing_env.yml | |
| pipeline_directory: ./example/preprocess | |
| pipeline_config: ./pipelines/config/deeprvat_preprocess_config.yaml | |
| dry_run: false | |
| download_fasta_data: true | |
| fasta_download_path: ./example/preprocess/workdir/reference | |
| # Annotation Pipeline | |
| Smoke-Annotation-Pipeline: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/annotations.snakefile | |
| environment_file: ./deeprvat_annotations.yml | |
| pipeline_config: ./pipelines/config/deeprvat_annotation_config.yaml | |
| pipeline_directory: ./example/annotations |