matching/project.yaml at main · opensafely-actions/matching · GitHub

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version: "4.0"

actions:
  # These actions are copied-and-pasted into README.md for user-facing documentation.
  # If you change them here, then please change them there.
  generate_cases:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_cases.py --output output/cases.arrow
    outputs:
      highly_sensitive:
        dataset: output/cases.arrow

  generate_controls:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_controls.py --output output/controls.arrow
    outputs:
      highly_sensitive:
        dataset: output/controls.arrow

  match:
    needs: [generate_cases, generate_controls]
    run: >
      python:v2 python -m osmatching.__main__
      --cases output/cases.arrow
      --controls output/controls.arrow
    config:
      matches_per_case: 3
      match_variables:
        sex: category
        age: 5
      index_date_variable: indexdate
      closest_match_variables:
        - age
      generate_match_index_date: no_offset
    outputs:
      highly_sensitive:
        matched_cases: output/matched_cases.arrow
        matched_controls: output/matched_matches.arrow
        matched_combined: output/matched_combined.arrow
      moderately_sensitive:
        report: output/matching_report.txt

  write_config:
    run: python:v2 analysis/write_matching_config.py
    needs: [generate_cases, generate_controls]
    outputs:
      moderately_sensitive:
        config: output/config.json

  match_with_config_file:
    run: >
      python:v2 python -m osmatching.__main__
      --cases output/cases.arrow
      --controls output/controls.arrow
      --config-file output/config.json
    needs: [write_config, generate_cases, generate_controls]
    outputs:
      highly_sensitive:
        matched_cases: output/matched_cases_with_config_file.arrow
        matched_controls: output/matched_matches_with_config_file.arrow
        matched_combined: output/matched_combined_with_config_file.arrow
      moderately_sensitive:
        report: output/matching_report_with_config_file.txt