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
outputs:
highly_sensitive:
cohort: output/input.csv
run_model:
run: r:latest analysis/model.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
count_by_region: output/qfit_by_region.csv
qfits_by_region: output/qfits_by_region.png
fobts_by_region: output/fobts_by_region.png
fobts_by_region_cat: output/fobts_by_region_cat.png
fobts_by_region_cat_fit: output/fobts_by_region_cat_fit.png
qfits_by_region_near_10: output/qfits_by_region_near_10.png
qfit_months_by_region: output/qfit_months_by_region.png
qfit_rmarkdown:
run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis.Rmd", output_dir = "output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
qfit_html: output/qfit_analysis.html
qfit_region_rmarkdown:
run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis_region.Rmd", output_dir = "output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
cum_prop_data: output/cum_prop_data.csv
cum_prop_graph: output/cum_prop_graph.png
qfit_html: output/qfit_analysis_region.html
qfit_region_rmarkdown_no_suppress:
run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis_region.Rmd", output_dir = "output", output_file = "qfit_analysis_region_no_suppress.html", params = list(suppress_if_le = FALSE))'
needs: [generate_study_population]
outputs:
moderately_sensitive:
qfit_html: output/qfit_analysis_region_no_suppress.html
qfit_check_new_data:
run: r:latest -e 'rmarkdown::render("analysis/check_new_fit_data.Rmd", output_dir = "output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
qfit_html: output/check_new_fit_data.html