Merge branch 'main' of github.com:PMBio/deeprvat into main

.github/workflows/code-tests.yml

@@ -0,0 +1,24 @@
+name: DeepRVAT code test runner
+run-name: DeepRVAT Code Tests 🧑🏼‍💻✅
+on: [ push ]
+
+jobs:
+  DeepRVAT-Tests-Runner-Preprocessing:
+    uses: ./.github/workflows/run-pytest.yml
+    with:
+      environment_file: ./deeprvat_preprocessing_env.yml
+      test_path: ./tests/preprocessing
+
+  DeepRVAT-Tests-Runner-Annotations:
+    uses: ./.github/workflows/run-pytest.yml
+    with:
+      environment_file: ./deeprvat_annotations.yml
+      test_path: ./tests/annotations
+      parallel_tests: true
+
+  DeepRVAT-Tests-Runner:
+    uses: ./.github/workflows/run-pytest.yml
+    with:
+      environment_file: ./deeprvat_env_no_gpu.yml
+      parallel_tests: true
+      test_path: ./tests/deeprvat

.github/workflows/pipeline-tests.yml

@@ -0,0 +1,155 @@
+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