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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_02qNwbSXwWDZsLaCA1ZXHX:
run: >
cohortextractor:latest generate_codelist_report
--codelist-path=codelist.csv
--start-date=2019-09-01
--end-date=2022-07-06
--output-dir output/02qNwbSXwWDZsLaCA1ZXHX
outputs:
moderately_sensitive:
table: output/02qNwbSXwWDZsLaCA1ZXHX/counts_per_*.csv
list_sizes: output/02qNwbSXwWDZsLaCA1ZXHX/list_sizes.csv
patient_count_table: output/02qNwbSXwWDZsLaCA1ZXHX/patient_count.csv
measures_02qNwbSXwWDZsLaCA1ZXHX:
run: >
python:latest python analysis/generate_measures.py
--start-date=2019-09-01
--end-date=2022-07-06
--output-dir output/02qNwbSXwWDZsLaCA1ZXHX
--low-count-threshold 100
--rounding-base 10
needs: [codelist_report_02qNwbSXwWDZsLaCA1ZXHX]
outputs:
moderately_sensitive:
measure: output/02qNwbSXwWDZsLaCA1ZXHX/measure_counts_per_week_per_practice.csv
events_count_table: output/02qNwbSXwWDZsLaCA1ZXHX/for_release/event_counts.csv
practice_count_table: output/02qNwbSXwWDZsLaCA1ZXHX/for_release/practice_count.csv
top_5_table_02qNwbSXwWDZsLaCA1ZXHX:
run: >
python:latest python analysis/top_codes_table.py
--start-date=2019-09-01
--end-date=2022-07-06
--output-dir output/02qNwbSXwWDZsLaCA1ZXHX
--low-count-threshold 100
--rounding-base 10
needs: [codelist_report_02qNwbSXwWDZsLaCA1ZXHX]
outputs:
moderately_sensitive:
table: output/02qNwbSXwWDZsLaCA1ZXHX/for_release/top_5_code_table.csv
deciles_charts_02qNwbSXwWDZsLaCA1ZXHX:
run: >
deciles-charts:v0.0.24
--input-files output/02qNwbSXwWDZsLaCA1ZXHX/measure_counts_per_week_per_practice.csv
--output-dir output/02qNwbSXwWDZsLaCA1ZXHX/for_release
config:
show_outer_percentiles: false
tables:
output: false
charts:
output: true
needs: [measures_02qNwbSXwWDZsLaCA1ZXHX]
outputs:
moderately_sensitive:
deciles_charts: output/02qNwbSXwWDZsLaCA1ZXHX/for_release/deciles_*.*