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pipeline-tests.yml
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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