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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input.feather
generate_study_population_derived_bmi:
run: cohortextractor:latest generate_cohort --study-definition study_definition_derived_bmi --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_derived_bmi.feather
generate_study_population_recorded_bmi:
run: cohortextractor:latest generate_cohort --study-definition study_definition_recorded_bmi --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_recorded_bmi.feather
generate_study_population_snomed_hw:
run: cohortextractor:latest generate_cohort --study-definition study_definition_snomed_hw --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_snomed_hw.feather
generate_study_population_ctv3_hw:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ctv3_hw --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_ctv3_hw.feather
preprocess_derived_bmi_input:
run: python:latest python analysis/preprocess_bmi_inputs.py "derived_bmi" --output-format feather
needs: [generate_study_population_derived_bmi]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_derived_bmi.feather
preprocess_recorded_bmi_input:
run: python:latest python analysis/preprocess_bmi_inputs.py "recorded_bmi" --output-format feather
needs: [generate_study_population_recorded_bmi]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_recorded_bmi.feather
preprocess_computed_bmi_input:
run: python:latest python analysis/preprocess_hw_inputs.py "height" "weight" "snomed" "computed_bmi" --output-format feather
needs: [generate_study_population_snomed_hw]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_computed_bmi.feather
preprocess_backend_computed_bmi_input:
run: python:latest python analysis/preprocess_hw_inputs.py "height_backend" "weight_backend" "ctv3" "backend_computed_bmi" --output-format feather
needs: [generate_study_population_ctv3_hw]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed_backend_computed_bmi.feather
join_cohorts:
run: >
cohort-joiner:v0.0.35
--lhs output/data/input_processed*.feather
--rhs output/data/input.feather
--output-dir output/joined
needs: [generate_study_population, preprocess_derived_bmi_input, preprocess_recorded_bmi_input, preprocess_computed_bmi_input, preprocess_backend_computed_bmi_input]
outputs:
highly_sensitive:
cohort: output/joined/input_processed*.feather
preprocess_age_dates:
run: python:latest python analysis/preprocess_age_dates.py --output-format feather
needs: [join_cohorts]
outputs:
highly_sensitive:
cohort1: output/joined/input_processed_backend_computed_bmi.feather
cohort2: output/joined/input_processed_computed_bmi.feather
cohort3: output/joined/input_processed_derived_bmi.feather
cohort4: output/joined/input_processed_recorded_bmi.feather
execute_validation_analyses_derived_bmi:
run: python:latest python analysis/validation_script_single_definition.py "derived_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/derived_bmi/*.csv
execute_validation_analyses_recorded_bmi:
run: python:latest python analysis/validation_script_single_definition.py "recorded_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/recorded_bmi/*.csv
execute_validation_analyses_computed_bmi:
run: python:latest python analysis/validation_script_single_definition.py "computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/computed_bmi/*.csv
execute_validation_analyses_backend_computed_bmi:
run: python:latest python analysis/validation_script_single_definition.py "backend_computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/backend_computed_bmi/*.csv
execute_validation_analyses_high_computed_bmi:
run: python:latest python analysis/validation_script_high_bmi.py "computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/high_computed_bmi/*.csv
execute_validation_analyses_high_backend_computed_bmi:
run: python:latest python analysis/validation_script_high_bmi.py "backend_computed_bmi"
needs: [preprocess_age_dates]
outputs:
moderately_sensitive:
tables: output/validation/tables/high_backend_computed_bmi/*.csv