generated from opensafely/research-template
/
project.yaml
286 lines (247 loc) · 9.07 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_pop_covdischarged:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covdischarged
outputs:
highly_sensitive:
cohort: output/input_covdischarged.csv
generate_study_pop_pneum2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneum2019
outputs:
highly_sensitive:
cohort: output/input_pneum2019.csv
generate_study_pop_flu2017_19:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flu2017_19
outputs:
highly_sensitive:
cohort: output/input_flu2017_19.csv
generate_2019pool02:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool02
outputs:
highly_sensitive:
cohort: output/input_2019pool02.csv
generate_2019pool02_ALT:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019 --index-date-range "2019-02-01"
outputs:
highly_sensitive:
cohort: output/input_2019_2019-02-01.csv
generate_2019pool03:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool03
outputs:
highly_sensitive:
cohort: output/input_2019pool03.csv
generate_2019pool04:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool04
outputs:
highly_sensitive:
cohort: output/input_2019pool04.csv
generate_2019pool05:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool05
outputs:
highly_sensitive:
cohort: output/input_2019pool05.csv
generate_2019pool06:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool06
outputs:
highly_sensitive:
cohort: output/input_2019pool06.csv
generate_2019pool07:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool07
outputs:
highly_sensitive:
cohort: output/input_2019pool07.csv
generate_2019pool08:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool08
outputs:
highly_sensitive:
cohort: output/input_2019pool08.csv
generate_2019pool09:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool09
outputs:
highly_sensitive:
cohort: output/input_2019pool09.csv
generate_2019pool10:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool10
outputs:
highly_sensitive:
cohort: output/input_2019pool10.csv
generate_2019pool11:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool11
outputs:
highly_sensitive:
cohort: output/input_2019pool11.csv
generate_2019pool12:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool12
outputs:
highly_sensitive:
cohort: output/input_2019pool12.csv
create_covid:
run: stata-mp:latest analysis/cr_create_analysis_dataset.do COVID
needs: [generate_study_pop_covdischarged]
outputs:
highly_sensitive:
cohort: analysis/cr_create_analysis_dataset_COVID.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_dataset_COVID.log
create_pneum2019:
run: stata-mp:latest analysis/cr_create_analysis_dataset.do PNEUM
needs: [generate_study_pop_pneum2019]
outputs:
highly_sensitive:
cohort: analysis/cr_create_analysis_dataset_PNEUM.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_dataset_PNEUM.log
create_flu2017_19:
run: stata-mp:latest analysis/cr_create_analysis_dataset.do FLU
needs: [generate_study_pop_flu2017_19]
outputs:
highly_sensitive:
cohort: analysis/cr_create_analysis_dataset_FLU.dta
moderately_sensitive:
log: analysis/output/cr_create_analysis_dataset_FLU.log
create_2019pool02:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 02
needs: [generate_2019pool02]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_02.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_02.log
create_2019pool03:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 03
needs: [generate_2019pool03]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_03.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_03.log
create_2019pool04:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 04
needs: [generate_2019pool04]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_04.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_04.log
create_2019pool05:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 05
needs: [generate_2019pool05]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_05.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_05.log
create_2019pool06:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 06
needs: [generate_2019pool06]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_06.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_06.log
create_2019pool07:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 07
needs: [generate_2019pool07]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_07.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_07.log
create_2019pool08:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 08
needs: [generate_2019pool08]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_08.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_08.log
create_2019pool09:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 09
needs: [generate_2019pool09]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_09.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_09.log
create_2019pool10:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 10
needs: [generate_2019pool10]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_10.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_10.log
create_2019pool11:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 11
needs: [generate_2019pool11]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_11.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_11.log
create_2019pool12:
run: stata-mp:latest analysis/cr_create_2019pool_data.do 12
needs: [generate_2019pool12]
outputs:
highly_sensitive:
cohort: analysis/cr_create_2019pool_data_12.dta
moderately_sensitive:
log: analysis/output/cr_create_2019pool_data_12.log
getmatches2019:
run: stata-mp:latest analysis/cr_getmatches2019.do
needs:
- create_covid
- create_2019pool02
- create_2019pool03
- create_2019pool04
- create_2019pool05
- create_2019pool06
- create_2019pool07
- create_2019pool08
- create_2019pool09
- create_2019pool10
- create_2019pool11
- create_2019pool12
outputs:
highly_sensitive:
cohort: analysis/cr_getmatches2019.dta
moderately_sensitive:
log: analysis/output/cr_getmatches2019.log
appenddata:
run: stata-mp:latest analysis/cr_append_process_data.do
needs:
- create_covid
- create_pneum2019
- create_flu2017_19
- getmatches2019
outputs:
highly_sensitive:
cohort: analysis/cr_append_process_data.dta
moderately_sensitive:
log: analysis/output/cr_append_process_data.log
andescriptives_models:
run: stata-mp:latest analysis/model_descriptives_models.do
needs:
- generate_study_pop_covdischarged
- appenddata
outputs:
moderately_sensitive:
logs: analysis/output/*.log
tables: analysis/output/an_*.txt
figures: analysis/output/an_cumulativeincidence*.svg
timefig: analysis/output/an_desc*.svg
models: analysis/output/models/an_cox*.ster
anprocess_forestplots:
run: stata-mp:latest analysis/model_forestplots.do
needs: [andescriptives_models]
outputs:
moderately_sensitive:
graphs: analysis/output/an_processout_*.svg
run_model:
run: stata-mp:latest analysis/model.do
needs: [generate_study_pop_covdischarged]
outputs:
moderately_sensitive:
log: logs/model.log