predoc/dvc.yaml at master · babelomics/predoc · GitHub

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stages:
  retrieve_raw_omop_data:
    cmd: ./predoc/retrieve_raw_omop_data.sh
    deps:
    - predoc/retrieve_raw_omop_data.sh
    outs:
    - data/omop/raw
  clean_raw_data:
    cmd: ./.venv/bin/python ./predoc/clean_raw_data.py
    params:
    - ban_codes
    deps:
    - data/omop/raw
    - predoc/clean_raw_data.py
    outs:
    - data/omop/rare
  adapt_omop:
    cmd: ./.venv/bin/python ./predoc/adapt_omop.py
    params:
    - target_diagnosis_concept_id
    deps:
    - data/omop/rare
    - predoc/adapt_omop.py
    outs:
    - data/omop/done
  train_OMOP:
    cmd: ./predoc/train_OMOP.sh
    deps:
    - data/omop/done
    - predoc/clean_raw_wrapper.py
    - predoc/generate_dummies.py
    - predoc/train_L2orEBM.py
    - predoc/train_OMOP.sh
    outs:
    - data/omop/train
  simulate_OMOP:
    cmd: ./predoc/simulate_OMOP.sh
    deps:
    - data/omop/train
    - predoc/clean_raw_wrapper.py
    - predoc/generate_dummies.py
    - predoc/simulate_OMOP.sh
    - predoc/simulate_dump_predictions_raw_parallel.py
    outs:
    - data/omop/simulate
  validate_OMOP:
    cmd: ./predoc/validate_OMOP.sh
    deps:
    - data/omop/simulate
    - data/omop/train
    - predoc/thresholds_parallel.py
    - predoc/validate_OMOP.sh
    outs:
    - data/omop/validate