generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2020-07-01 by month" --output-format=csv.gz --with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_*.csv.gz
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-08-01 to 2021-01-01 by month" --output-format=csv.gz --with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
# Gives until 2021-07-01. Only have ONS deaths until 2021-07-01
# generate_study_population_3:
# run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-02-01 to 2021-06-01 by month" --output-format=csv.gz --with-end-date-fix
# outputs:
# highly_sensitive:
# cohort: output/inpu*.csv.gz
# generate_study_population_end:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz --with-end-date-fix
# outputs:
# highly_sensitive:
# cohort: output/input_end.csv.gz
# join_cohorts_monthly:
# run: >
# cohort-joiner:v0.0.44
# --lhs output/input_20*.csv.gz
# --rhs output/input_end.csv.gz
# --output-dir output/joined
# needs: [
# generate_study_population_1,
# generate_study_population_2,
# generate_study_population_3,
# generate_study_population_end]
# outputs:
# highly_sensitive:
# cohort: output/joined/input_20*.csv.gz
generate_dataset_report:
run: >
dataset-report:v0.0.24
--input-files output/input_2021-01-01.csv.gz
--output-dir output
needs: [generate_study_population_2]
outputs:
moderately_sensitive:
dataset_report: output/input_2021-01-01.html
combined_input_files:
run: r:latest analysis/combine_input_files.R
needs: [generate_study_population_1, generate_study_population_2]
outputs:
highly_sensitive:
attrition: output/input_all.csv.gz
generate_first_outputs:
run: r:latest analysis/flucats_descriptive_basic.R
needs: [combined_input_files]
outputs:
moderately_sensitive:
attrition: output/attrition.csv
histogram_age: output/age_hist.png
date_plot: output/weekly_template.png
flucat_tables: output/flucat*.csv
sex_table: output/sex_table.csv
region_table: output/region_table.csv