generated from opensafely/research-template
/
project.yaml
85 lines (78 loc) · 3.42 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 1000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_measures_cohorts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-10-01 by month"
outputs:
highly_sensitive:
cohort1: output/input_measures_2019-02-01.csv
cohort2: output/input_measures_2019-03-01.csv
cohort3: output/input_measures_2019-04-01.csv
cohort4: output/input_measures_2019-05-01.csv
cohort5: output/input_measures_2019-06-01.csv
cohort6: output/input_measures_2019-07-01.csv
cohort7: output/input_measures_2019-08-01.csv
cohort8: output/input_measures_2019-09-01.csv
cohort9: output/input_measures_2019-10-01.csv
cohort10: output/input_measures_2019-11-01.csv
cohort11: output/input_measures_2019-12-01.csv
cohort12: output/input_measures_2020-01-01.csv
cohort13: output/input_measures_2020-02-01.csv
cohort14: output/input_measures_2020-03-01.csv
cohort15: output/input_measures_2020-04-01.csv
cohort16: output/input_measures_2020-05-01.csv
cohort17: output/input_measures_2020-06-01.csv
cohort18: output/input_measures_2020-07-01.csv
cohort19: output/input_measures_2020-08-01.csv
cohort20: output/input_measures_2020-09-01.csv
cohort21: output/input_measures_2020-10-01.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures
needs: [generate_measures_cohorts]
outputs:
moderately_sensitive:
measure1: output/measure_covid_death_all.csv
measure2: output/measure_covid_death_sex.csv
measure3: output/measure_covid_death_age.csv
measure4: output/measure_covid_death_sex_age.csv
measure5: output/measure_allcause_death_all.csv
measure6: output/measure_allcause_death_sex.csv
measure7: output/measure_allcause_death_age.csv
measure8: output/measure_allcause_death_sex_age.csv
01_data_management:
run: r:latest analysis/01_data_management.R
needs: [generate_cohort]
outputs:
highly_sensitive:
data: data/study_population.csv
02_baseline_characteristics:
run: r:latest analysis/02_baseline_characteristics.R
needs: [generate_cohort, 01_data_management]
outputs:
moderately_sensitive:
table_1: analysis/outfiles/table_1.txt
03_descriptive_mortality_rates:
run: r:latest analysis/03_descriptive_mortality_rates.R
needs: [generate_measures]
outputs:
moderately_sensitive:
table_2a: analysis/outfiles/table_2a.txt
table_2b: analysis/outfiles/table_2b.txt
table_2c: analysis/outfiles/table_2c.txt
table_2d: analysis/outfiles/table_2d.txt
table_3a: analysis/outfiles/table_3a.txt
table_3b: analysis/outfiles/table_3b.txt
table_3c: analysis/outfiles/table_3c.txt
table_3d: analysis/outfiles/table_3d.txt
plot_1a: analysis/outfiles/plot_1a.png
plot_1b: analysis/outfiles/plot_1b.png
plot_1c: analysis/outfiles/plot_1c.png
plot_2a: analysis/outfiles/plot_2a.png
plot_2b: analysis/outfiles/plot_2b.png
plot_2c: analysis/outfiles/plot_2c.png