generated from opensafely/research-template
/
project.yaml
67 lines (58 loc) · 1.96 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 10000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
feasibility:
run: stata-mp:latest analysis/00_Test_runs_and_feasibility.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: logs/00_Test_runs_and_feasibility.log
# figure1: output/00_spells.svg
crMAIN:
run: stata-mp:latest analysis/cr_analysis_dataset.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: logs/cr_analysis_dataset.log
highly_sensitive:
data: analysis/cr_analysis_dataset.dta
anCASE:
run: stata-mp:latest analysis/an_ccount_crude.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_ccount_crude.log
figure1: output/tpp_sgss_counts.svg
figure2: output/tpp_type_counts.svg
figure3: output/tpp_fp.svg
anCOX:
run: stata-mp:latest analysis/an_cox_models.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_cox_models.log
# figure1: output/unadj_cox_haz.svg
figure1: output/unadj_utla_cox_haz.svg
figure2: output/utla_haz.svg
figure3: output/unadj_utla_cox_week.svg
figure4: output/unadj_utla_cox_week_nl.svg
figure5: output/reg_utla_cox_haz.svg
figure6: output/unadj_utla_sgss_haz.svg
figure7: output/unadj_utla_sgss_week.svg
figure8: output/unadj_utla_sgss_week_nl.svg
run_all:
needs: [feasibility]
# In order to be valid this action needs to define a run commmand and some
# output. We don't really care what these are but the below does the trick.
# In a future release of the platform, this special action won't need to be
# defined at all.
run: cohortextractor:latest --version
outputs:
moderately_sensitive:
whatever: project.yaml