generated from opensafely/covid-vaccine-research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
# gen_std_popn:
# run: cohortextractor:latest generate_cohort --study-definition study_definition
# outputs:
# highly_sensitive:
# cohort: output/input.csv
# run_model:
# run: r:latest analysis/1-rcmdbatch.R # 1-basic-rd.R
# needs: [gen_std_popn]
# outputs:
# moderately_sensitive:
# figure1: output/plots/pt_plot.png
# # figure2: output/plots/four_plot.png
# log: logs/1-basic-rd.log
gen_std_popn_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
outputs:
highly_sensitive:
cohort: output/input_2.csv
run_model_2:
run: r:latest analysis/2-rcmdbatch.R # 2-basic-rd.R
needs: [gen_std_popn_2]
outputs:
moderately_sensitive:
figure1: output/pt_plot_week_1.png
figure2: output/pt_plot_week_2.png
figure3: output/pt_plot_week_3.png
figure4: output/pt_plot_week_4.png
figure5: output/pt_plot_week_5.png
figure6: output/pt_plot_week_6.png
figure7: output/pt_plot_week_7.png
figure8: output/pt_plot_week_8.png
log: logs/2-basic-rd.log
# gen_std_popn_by_week:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_2 --index-date-range "2020-12-08 to 2021-02-01 by week" --output-dir=output/measures
# outputs:
# highly_sensitive:
# cohort: output/measures/input_by_week_*.csv
#