/
project.yaml
85 lines (74 loc) · 2.15 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
crMAIN:
run: stata-mp:latest analysis/cr_main.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: logs/cr_main.log
highly_sensitive:
data: output/main.dta
anSUMM:
run: stata-mp:latest analysis/an_summary.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_summary.log
figure1: output/sgtf_perc_region.svg
figure2: output/sgtf_perc_region.pdf
anTAB1:
run: stata-mp:latest analysis/an_table1.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_table1.log
table1text: output/table1.txt
table1xlsx: output/table1.xlsx
figure1: output/time_ae_hist.svg
figure2: output/date_ae_hist.svg
figure3: output/date_ae_hist1.svg
figure4: output/ae_hist.svg
figure5: output/ae_kden.svg
anCOX:
run: stata-mp:latest analysis/an_cox.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_cox.log
figure1: output/cox_shoen.svg
figure2: output/cox_km.svg
figure3: output/cox_cumhaz.svg
figure4: output/cox_haz.svg
table1text: output/table2.txt
table1xlsx: output/table2.xlsx
crIMP:
run: stata-mp:latest analysis/cr_imputed.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/cr_imputed.log
highly_sensitive:
data: output/main_imputed.dta
anCOX_IMP:
run: stata-mp:latest analysis/an_cox_imputed.do
needs: [crIMP]
outputs:
moderately_sensitive:
log: logs/an_cox_imputed.log
highly_sensitive:
data2: output/an_imputed_eth2.ster
anRISK:
run: stata-mp:latest analysis/an_risk.do
needs: [crMAIN]
outputs:
moderately_sensitive:
log: logs/an_risk.log
table1text: output/table3.txt
table1xlsx: output/table3.xlsx