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:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population
outputs:
highly_sensitive:
cohort: output/input_general_population.csv
generate_study_population_covid_primarycare:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_primarycare
outputs:
highly_sensitive:
cohort: output/input_covid_primarycare.csv
generate_study_population_covid_SGSS:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_SGSS
outputs:
highly_sensitive:
cohort: output/input_covid_SGSS.csv
generate_study_population_covid_admission:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_admission
outputs:
highly_sensitive:
cohort: output/input_covid_admission.csv
# generate_study_population_covid_icu:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_icu
# outputs:
# highly_sensitive:
# cohort: output/input_covid_icu.csv
generate_study_population_covid_death_ons:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_death_ons
outputs:
highly_sensitive:
cohort: output/input_covid_death_ons.csv
generate_study_population_covid_death_cpns:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_death_cpns
outputs:
highly_sensitive:
cohort: output/input_covid_death_cpns.csv
process:
run: r:latest analysis/process.R
needs: [generate_study_population_covid_primarycare, generate_study_population_covid_SGSS,generate_study_population_covid_admission,generate_study_population_covid_death_ons,generate_study_population_covid_death_cpns]
outputs:
highly_sensitive:
cohort1.1: output/case_covid_infection.csv
cohort1.2: output/control_covid_infection.csv
cohort1.3: output/case_covid_infection_*.csv # for monthly matching
cohort2: output/case_covid_admission.csv
cohort3: output/case_covid_icu_death.csv
matching:
run: python:latest python analysis/matching_case_control.py
needs: [generate_study_population, process]
outputs:
moderately_sensitive:
matching_report1: output/matching_report_general_population_infection.txt
matching_report2: output/matching_report_infection_hosp.txt
matching_report3: output/matching_report_hosp_icu_death.txt
highly_sensitive:
combined1: output/matched_combined_general_population_infection.csv
combined2: output/matched_combined_infection_hosp.csv
combined3: output/matched_combined_hosp_icu_death.csv
## monthly matching datasets
generate_study_population_month:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population --index-date-range "2020-02-01 to 2021-12-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
exclusion:
run: r:latest analysis/exclusion.R
needs: [process, generate_study_population_month]
outputs:
highly_sensitive:
cohort4: output/control_general_population_*.csv