DeepRVAT Pipeline Tests 🧬🧪💻🧑🔬 #485
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: DeepRVAT Pipeline Tests | |
| run-name: DeepRVAT Pipeline Tests 🧬🧪💻🧑🔬 | |
| on: [ push ] | |
| jobs: | |
| # Config Setup | |
| Smoke-GenerateConfig-Training: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./example/config/deeprvat_input_training_config.yaml ./example/ | |
| Smoke-GenerateConfig-Training-AssociationTesting: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/training_association_testing.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./example/config/deeprvat_input_config.yaml ./example/ | |
| Smoke-GenerateConfig-PreTrained: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./example/config/deeprvat_input_pretrained_models_config.yaml ./example/ && ln -s $GITHUB_WORKSPACE/pretrained_models ./example/ | |
| # Training Pipeline | |
| Smoke-RunTraining: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/ | |
| Pipeline-Tests-RunTraining: | |
| needs: [Smoke-RunTraining, Reference-Output-Training] | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| download_training_outputs: true | |
| run_training_results_check: true | |
| Reference-Output-Training: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| branch: main | |
| pipeline_file: ./pipelines/run_training.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| upload_training_outputs: true | |
| Reference-Output-Pretrained: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| branch: main | |
| pipeline_file: ./pipelines/association_testing_pretrained.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| upload_pretrained_outputs: true | |
| Reference-Output-Pretrained-Regenie: | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| branch: main | |
| pipeline_file: ./pipelines/association_testing_pretrained_regenie.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| upload_regenie_outputs: true | |
| # 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: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/ | |
| Pipeline-Tests-Training-Association-Testing: | |
| needs: [Smoke-Association-Testing-Pretrained, Reference-Output-Pretrained] | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/association_testing_pretrained.snakefile | |
| environment_file: ./deeprvat_env_no_gpu.yml | |
| prerun_cmd: cp ./tests/deeprvat/pretrained/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| download_pretrained_outputs: true | |
| run_burden_results_check: true | |
| run_association_results_check: true | |
| # 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: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/ | |
| Pipeline-Tests-Association-Testing-Pretrained-Regenie: | |
| needs: [Smoke-Association-Testing-Pretrained-Regenie, Reference-Output-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: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/ | |
| dry_run: false | |
| download_regenie_outputs: true | |
| run_regenie_association_results_check: true | |
| # 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 | |
| prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/ | |
| 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 | |
| prerun_cmd: cp ./tests/deeprvat/training_association_testing/deeprvat_config.yaml ./example/ | |
| 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 | |
| prerun_cmd: cp ./tests/deeprvat/regenie/training_association_testing/deeprvat_config.yaml ./example/ | |
| 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 | |
| prerun_cmd: cp ./tests/deeprvat/regenie/training_association_testing/deeprvat_config.yaml ./example/ | |
| 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: cp ./tests/seed_gene_discovery/sg_discovery_config.yaml ./example/ | |
| 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: cp ./tests/seed_gene_discovery/sg_discovery_config.yaml ./example/ | |
| 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: ./example/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: ./example/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: ./example/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: ./example/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 | |
| prerun_cmd: | | |
| mkdir -pv ./example/preprocess/workdir/norm/variants && \ | |
| mkdir -pv ./example/preprocess/workdir/preprocessed && \ | |
| touch ./example/preprocess/workdir/preprocessed/genotypes.h5 && \ | |
| touch ./example/preprocess/workdir/norm/variants/variants.parquet | |
| pipeline_config: ./example/config/deeprvat_annotation_config.yaml | |
| pipeline_directory: ./example/annotations | |
| download_fasta_data: true | |
| fasta_download_path: ./example/annotations/reference | |
| Pipeline-Annotation: | |
| needs: Smoke-Annotation-Pipeline | |
| uses: ./.github/workflows/run-pipeline.yml | |
| with: | |
| pipeline_file: ./pipelines/annotations.snakefile | |
| environment_file: ./deeprvat_annotations.yml | |
| prerun_cmd: | | |
| mkdir ./example/annotations/repo_dir && \ | |
| bash deeprvat/annotations/setup_annotation_workflow.sh ./example/annotations/repo_dir faatpipe && \ | |
| wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.annotation.gtf.gz \ | |
| -O ./example/annotations/reference/gencode.v44.annotation.gtf.gz | |
| pipeline_directory: ./example/annotations | |
| pipeline_config: ./example/config/deeprvat_annotation_config_minimal.yaml | |
| dry_run: false | |
| download_fasta_data: true | |
| fasta_download_path: ./example/annotations/reference |