/
project.yaml
128 lines (115 loc) · 5.19 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_ethnicity_01GWJ26M2VQF6MFF7X3WF44C01:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--param end_date="2023-03-15"
--output-dir output/01GWJ26M2VQF6MFF7X3WF44C01 --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GWJ26M2VQF6MFF7X3WF44C01/input_ethnicity.csv.gz
generate_study_population_01GWJ26M2VQF6MFF7X3WF44C01:
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="5"
--param time_scale="years"
--param time_event="before"
--param codelist_2_comparison_date="end_date"
--param operator="AND"
--param population="adults"
--param breakdowns="sex,age,ethnicity,imd,region"
--index-date-range="2022-09-16 to 2023-03-15 by month"
--output-dir=output/01GWJ26M2VQF6MFF7X3WF44C01
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GWJ26M2VQF6MFF7X3WF44C01/input_*.csv.gz
join_cohorts_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
cohort-joiner:v0.0.38
--lhs output/01GWJ26M2VQF6MFF7X3WF44C01/input_20*.csv.gz
--rhs output/01GWJ26M2VQF6MFF7X3WF44C01/input_ethnicity.csv.gz
--output-dir output/01GWJ26M2VQF6MFF7X3WF44C01/joined
needs: [generate_study_population_01GWJ26M2VQF6MFF7X3WF44C01, generate_study_population_ethnicity_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
highly_sensitive:
cohort: output/01GWJ26M2VQF6MFF7X3WF44C01/joined/input_20*.csv.gz
generate_measures_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
python:latest -m analysis.measures
--breakdowns="sex,age,ethnicity,imd,region"
--input_dir="output/01GWJ26M2VQF6MFF7X3WF44C01/joined"
--measure="med_review"
needs: [join_cohorts_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
measure: output/01GWJ26M2VQF6MFF7X3WF44C01/joined/measure*rate.csv
decile_measure: output/01GWJ26M2VQF6MFF7X3WF44C01/joined/measure*rate_deciles.csv
top_5_table_01GWJ26M2VQF6MFF7X3WF44C01:
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/01GWJ26M2VQF6MFF7X3WF44C01"
needs: [generate_measures_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
tables: output/01GWJ26M2VQF6MFF7X3WF44C01/joined/top_5*.csv
deciles_chart_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
deciles-charts:v0.0.33
--input-files output/01GWJ26M2VQF6MFF7X3WF44C01/joined/measure_practice_rate_deciles.csv
--output-dir output/01GWJ26M2VQF6MFF7X3WF44C01/joined
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [generate_measures_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
deciles_charts: output/01GWJ26M2VQF6MFF7X3WF44C01/joined/deciles_*.*
plot_measure_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
python:latest python analysis/plot_measures.py
--breakdowns="sex,age,ethnicity,imd,region"
--output-dir output/01GWJ26M2VQF6MFF7X3WF44C01
needs: [generate_measures_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
measure: output/01GWJ26M2VQF6MFF7X3WF44C01/plot_measure*.png
event_counts_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
python:latest python analysis/event_counts.py --input_dir="output/01GWJ26M2VQF6MFF7X3WF44C01/joined" --output_dir="output/01GWJ26M2VQF6MFF7X3WF44C01"
needs: [join_cohorts_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
measure: output/01GWJ26M2VQF6MFF7X3WF44C01/event_counts.json
generate_report_01GWJ26M2VQF6MFF7X3WF44C01:
run: >
python:latest python analysis/render_report.py
--output-dir="output/01GWJ26M2VQF6MFF7X3WF44C01"
--report-title="OpenPrescribing Measure: Co-amoxiclav, cephalosporins and quinolones (numerato & Chronic obstructive pulmonary disease (COPD) codes"
--population="adults"
--breakdowns="sex,age,ethnicity,imd,region"
--codelist-1-name="OpenPrescribing Measure: Co-amoxiclav, cephalosporins and quinolones (numerato"
--codelist-2-name="Chronic obstructive pulmonary disease (COPD) codes"
--codelist-1-link="opensafely/co-amoxiclav-cephalosporins-and-quinolones/0d299a50"
--codelist-2-link="nhsd-primary-care-domain-refsets/copd_cod/20210127"
--time-value="5"
--time-scale="years"
--time-event="before"
--start-date="2022-09-16"
--end-date="2023-03-15"
needs: [event_counts_01GWJ26M2VQF6MFF7X3WF44C01, deciles_chart_01GWJ26M2VQF6MFF7X3WF44C01, top_5_table_01GWJ26M2VQF6MFF7X3WF44C01, plot_measure_01GWJ26M2VQF6MFF7X3WF44C01]
outputs:
moderately_sensitive:
notebook: output/01GWJ26M2VQF6MFF7X3WF44C01/report.html