generated from opensafely/research-template
/
project.yaml
59 lines (50 loc) · 1.91 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input.csv.gz
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_processed_day0.rds
data2: output/data/data_processed_day5.rds
data_properties_process_day0:
run: r:latest analysis/data_properties.R output/data/data_processed_day0.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_day0_skim.txt
txt2: output/data_properties/data_processed_day0_coltypes.txt
txt3: output/data_properties/data_processed_day0_tabulate.txt
data_properties_process_day5:
run: r:latest analysis/data_properties.R output/data/data_processed_day5.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_day5_skim.txt
txt2: output/data_properties/data_processed_day5_coltypes.txt
txt3: output/data_properties/data_processed_day5_tabulate.txt
table_1_day5:
run: r:latest analysis/table_1.R day5
needs: [data_process]
outputs:
highly_sensitive:
data: output/tables/table1_redacted_day5.rds
moderately_sensitive:
table: output/tables/table1_redacted_day5.html
cox_day5:
run: r:latest analysis/cox_models.R day5
needs: [data_process]
outputs:
highly_sensitive:
data: output/tables/cox_models_day5.rds
moderately_sensitive:
figure: output/figs/*_overlap_plot_day5.png.
table1: output/tables/cox_models_day5.csv
table2: output/tables/log_cox_models_day5.csv