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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
codelist_report_02q87lMmz98GXYLAAzgj0I:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelist.csv
--start-date=2019-09-01
--end-date=2022-06-08
--output-dir output/02q87lMmz98GXYLAAzgj0I
outputs:
moderately_sensitive:
table: output/02q87lMmz98GXYLAAzgj0I/counts_per_*.csv
list_sizes: output/02q87lMmz98GXYLAAzgj0I/list_sizes.csv
patient_count_table: output/02q87lMmz98GXYLAAzgj0I/patient_count.csv
measures_02q87lMmz98GXYLAAzgj0I:
run: python:latest python analysis/generate_measures.py output/02q87lMmz98GXYLAAzgj0I
needs: [codelist_report_02q87lMmz98GXYLAAzgj0I]
outputs:
moderately_sensitive:
measure: output/02q87lMmz98GXYLAAzgj0I/measure_counts_per_week_per_practice.csv
events_count_table: output/02q87lMmz98GXYLAAzgj0I/event_counts.csv
practice_count_table: output/02q87lMmz98GXYLAAzgj0I/practice_count.csv
top_5_table_02q87lMmz98GXYLAAzgj0I:
run: python:latest python analysis/top_codes_table.py output/02q87lMmz98GXYLAAzgj0I
needs: [codelist_report_02q87lMmz98GXYLAAzgj0I]
outputs:
moderately_sensitive:
table: output/02q87lMmz98GXYLAAzgj0I/top_5_code_table.csv
deciles_charts_02q87lMmz98GXYLAAzgj0I:
run: >
deciles-charts:v0.0.24
--input-files output/02q87lMmz98GXYLAAzgj0I/measure_counts_per_week_per_practice.csv
--output-dir output/02q87lMmz98GXYLAAzgj0I
config:
show_outer_percentiles: false
tables:
output: true
charts:
output: true
needs: [measures_02q87lMmz98GXYLAAzgj0I]
outputs:
moderately_sensitive:
deciles_charts: output/02q87lMmz98GXYLAAzgj0I/deciles_*.*