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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_flowchart:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart
outputs:
highly_sensitive:
cohort: output/input_flowchart.csv
flowchart_data:
run: stata-mp:latest analysis/100_flowchart.do
needs: [generate_study_population_flowchart, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/flowchart.log
table: output/flowchart/values.txt
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_study_population_pbc:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pbc
outputs:
highly_sensitive:
cohort: output/input_pbc.csv
generate_study_population_vacc:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc
outputs:
highly_sensitive:
cohort: output/input_vacc.csv
feasibility:
run: stata-mp:latest analysis/feasibility.do
needs: [generate_study_population, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/feasibility.log
table: output/tables/udca*.csv
#table_oba: output/tables/oba*.csv
extract_udca:
run: cohortextractor:latest generate_cohort --study-definition study_definition_additional
needs: [generate_study_population_pbc]
outputs:
highly_sensitive:
cohort: output/input_additional.csv
extract_udca_vacc:
run: cohortextractor:latest generate_cohort --study-definition study_definition_addvacc
needs: [generate_study_population_vacc]
outputs:
highly_sensitive:
cohort: output/input_addvacc.csv
prep_drug_data:
run: stata-mp:latest analysis/101_drug_prep.do
needs: [extract_udca, generate_study_population_pbc, extract_udca_vacc, generate_study_population_vacc]
outputs:
moderately_sensitive:
log: logs/drug_prep.log
highly_sensitive:
drug_data: output/time_varying_udca*.dta
drug_descriptives:
run: stata-mp:latest analysis/102_udca_descriptives.do
needs: [prep_drug_data, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/udca_descriptives.log
summary: output/tables/udca_descriptives.txt
time_varying_prep:
run: stata-mp:latest analysis/103_time_varying_prep.do
needs: [generate_study_population_pbc, prep_drug_data, extract_udca_vacc, generate_study_population_vacc]
outputs:
highly_sensitive:
datasets: output/tv*.dta
analysis: output/an_*.dta
moderately_sensitive:
log: logs/time_varying.log
baseline_tables:
run: stata-mp:latest analysis/104_baseline_tables.do
needs: [generate_study_population_pbc, generate_study_population_vacc]
outputs:
moderately_sensitive:
log: logs/baseline_tables.log
chars: output/tables/baseline*.csv
meds: output/tables/additional*.csv
analysis_plots:
run: stata-mp:latest analysis/105_analysis_plots.do
needs: [time_varying_prep]
outputs:
moderately_sensitive:
log: logs/analysis.log
chars: output/graphs/adjcurv*.svg
table: output/tables/cum_incidence.txt
analysis_models:
run: stata-mp:latest analysis/106_analysis_models.do
needs: [time_varying_prep]
outputs:
moderately_sensitive:
log: logs/analysis_models.log
tables: output/tables/cox*
graphs: output/graphs/schoenplot*.svg
km_plots: output/graphs/km*.svg