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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_ethnicity_01GX6SE1YQ45AH63X265TBPBTA:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--param end_date="2023-03-29"
--output-dir output/01GX6SE1YQ45AH63X265TBPBTA --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GX6SE1YQ45AH63X265TBPBTA/input_ethnicity.csv.gz
generate_study_population_01GX6SE1YQ45AH63X265TBPBTA:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--param codelist_1_path="interactive_codelists/codelist_1.csv"
--param codelist_1_type="medication"
--param codelist_2_path="interactive_codelists/codelist_2.csv"
--param codelist_2_type="event"
--param codelist_1_frequency="monthly"
--param time_value="10"
--param time_scale="years"
--param time_event="before"
--param codelist_2_comparison_date="end_date"
--param operator="AND"
--param population="all"
--param breakdowns="age,ethnicity,imd,region,sex"
--index-date-range="2019-09-01 to 2023-03-29 by month"
--output-dir=output/01GX6SE1YQ45AH63X265TBPBTA
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GX6SE1YQ45AH63X265TBPBTA/input_*.csv.gz
join_cohorts_01GX6SE1YQ45AH63X265TBPBTA:
run: >
cohort-joiner:v0.0.38
--lhs output/01GX6SE1YQ45AH63X265TBPBTA/input_20*.csv.gz
--rhs output/01GX6SE1YQ45AH63X265TBPBTA/input_ethnicity.csv.gz
--output-dir output/01GX6SE1YQ45AH63X265TBPBTA/joined
needs: [generate_study_population_01GX6SE1YQ45AH63X265TBPBTA, generate_study_population_ethnicity_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
highly_sensitive:
cohort: output/01GX6SE1YQ45AH63X265TBPBTA/joined/input_20*.csv.gz
generate_measures_01GX6SE1YQ45AH63X265TBPBTA:
run: >
python:latest -m analysis.measures
--breakdowns="age,ethnicity,imd,region,sex"
--input_dir="output/01GX6SE1YQ45AH63X265TBPBTA/joined"
--measure="med_review"
needs: [join_cohorts_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
measure: output/01GX6SE1YQ45AH63X265TBPBTA/joined/measure*rate.csv
decile_measure: output/01GX6SE1YQ45AH63X265TBPBTA/joined/measure*rate_deciles.csv
top_5_table_01GX6SE1YQ45AH63X265TBPBTA:
run: >
python:latest python analysis/top_5.py
--codelist-1-path="interactive_codelists/codelist_1.csv"
--codelist-2-path="interactive_codelists/codelist_2.csv"
--output-dir="output/01GX6SE1YQ45AH63X265TBPBTA"
needs: [generate_measures_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
tables: output/01GX6SE1YQ45AH63X265TBPBTA/joined/top_5*.csv
deciles_chart_01GX6SE1YQ45AH63X265TBPBTA:
run: >
deciles-charts:v0.0.33
--input-files output/01GX6SE1YQ45AH63X265TBPBTA/joined/measure_practice_rate_deciles.csv
--output-dir output/01GX6SE1YQ45AH63X265TBPBTA/joined
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [generate_measures_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
deciles_charts: output/01GX6SE1YQ45AH63X265TBPBTA/joined/deciles_*.*
plot_measure_01GX6SE1YQ45AH63X265TBPBTA:
run: >
python:latest python analysis/plot_measures.py
--breakdowns="age,ethnicity,imd,region,sex"
--output-dir output/01GX6SE1YQ45AH63X265TBPBTA
needs: [generate_measures_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
measure: output/01GX6SE1YQ45AH63X265TBPBTA/plot_measure*.png
event_counts_01GX6SE1YQ45AH63X265TBPBTA:
run: >
python:latest python analysis/event_counts.py --input_dir="output/01GX6SE1YQ45AH63X265TBPBTA/joined" --output_dir="output/01GX6SE1YQ45AH63X265TBPBTA"
needs: [join_cohorts_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
measure: output/01GX6SE1YQ45AH63X265TBPBTA/event_counts.json
generate_report_01GX6SE1YQ45AH63X265TBPBTA:
run: >
python:latest python analysis/render_report.py
--output-dir="output/01GX6SE1YQ45AH63X265TBPBTA"
--report-title="Phenoxymethylpenicillin (oral preparations only) & Sickle (SPL-AtRiskv4) (SNOMED CT)"
--population="all"
--breakdowns="age,ethnicity,imd,region,sex"
--codelist-1-name="Phenoxymethylpenicillin (oral preparations only)"
--codelist-2-name="Sickle (SPL-AtRiskv4) (SNOMED CT)"
--codelist-1-link="opensafely/phenoxymethylpenicillin-oral-preparations-only/14b427f8"
--codelist-2-link="nhsd/sickle-spl-atriskv4-snomed-ct/7083ed37"
--time-value="10"
--time-scale="years"
--time-event="before"
--start-date="2019-09-01"
--end-date="2023-03-29"
needs: [event_counts_01GX6SE1YQ45AH63X265TBPBTA, deciles_chart_01GX6SE1YQ45AH63X265TBPBTA, top_5_table_01GX6SE1YQ45AH63X265TBPBTA, plot_measure_01GX6SE1YQ45AH63X265TBPBTA]
outputs:
moderately_sensitive:
notebook: output/01GX6SE1YQ45AH63X265TBPBTA/report.html