generated from opensafely/research-template
/
project.yaml
227 lines (201 loc) · 7.96 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
## # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create-project.R
## Edit and run create-project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Extract admission date
## # # # # # # # # # # # # # # # # # # #
extract_isaric_admission1:
run: databuilder:v0 generate-dataset 'analysis/dataset_definition_isaric.py' --dummy-tables
'dummy-tables/' --output 'output/admissions/isaric_admission1.csv.gz'
needs: []
outputs:
highly_sensitive:
csv: output/admissions/isaric_admission1.csv.gz
process_isaric:
run: r:latest analysis/process_isaric.R
needs:
- extract_isaric_admission1
outputs:
highly_sensitive:
rds: output/admissions/processed_isaric.rds
moderately_sensitive:
txt: output/admissions/isaric_raw_skim.txt
extract_sus_methodA_admission1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission1.csv.gz --param admission_number=1
--param admission_method=A
needs: []
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission1.csv.gz
extract_sus_methodA_admission2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission2.csv.gz --param admission_number=2
--param admission_method=A
needs:
- extract_sus_methodA_admission1
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission2.csv.gz
extract_sus_methodA_admission3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission3.csv.gz --param admission_number=3
--param admission_method=A
needs:
- extract_sus_methodA_admission2
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission3.csv.gz
extract_sus_methodA_admission4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission4.csv.gz --param admission_number=4
--param admission_method=A
needs:
- extract_sus_methodA_admission3
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission4.csv.gz
extract_sus_methodA_admission5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission5.csv.gz --param admission_number=5
--param admission_method=A
needs:
- extract_sus_methodA_admission4
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission5.csv.gz
extract_sus_methodB_admission1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission1.csv.gz --param admission_number=1
--param admission_method=B
needs: []
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission1.csv.gz
extract_sus_methodB_admission2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission2.csv.gz --param admission_number=2
--param admission_method=B
needs:
- extract_sus_methodB_admission1
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission2.csv.gz
extract_sus_methodB_admission3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission3.csv.gz --param admission_number=3
--param admission_method=B
needs:
- extract_sus_methodB_admission2
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission3.csv.gz
extract_sus_methodB_admission4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission4.csv.gz --param admission_number=4
--param admission_method=B
needs:
- extract_sus_methodB_admission3
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission4.csv.gz
extract_sus_methodB_admission5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission5.csv.gz --param admission_number=5
--param admission_method=B
needs:
- extract_sus_methodB_admission4
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission5.csv.gz
extract_sus_methodC_admission1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission1.csv.gz --param admission_number=1
--param admission_method=C
needs: []
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission1.csv.gz
extract_sus_methodC_admission2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission2.csv.gz --param admission_number=2
--param admission_method=C
needs:
- extract_sus_methodC_admission1
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission2.csv.gz
extract_sus_methodC_admission3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission3.csv.gz --param admission_number=3
--param admission_method=C
needs:
- extract_sus_methodC_admission2
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission3.csv.gz
extract_sus_methodC_admission4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission4.csv.gz --param admission_number=4
--param admission_method=C
needs:
- extract_sus_methodC_admission3
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission4.csv.gz
extract_sus_methodC_admission5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission5.csv.gz --param admission_number=5
--param admission_method=C
needs:
- extract_sus_methodC_admission4
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission5.csv.gz
process_sus:
run: r:latest analysis/process_sus.R
needs:
- extract_sus_methodA_admission1
- extract_sus_methodA_admission2
- extract_sus_methodA_admission3
- extract_sus_methodA_admission4
- extract_sus_methodA_admission5
- extract_sus_methodB_admission1
- extract_sus_methodB_admission2
- extract_sus_methodB_admission3
- extract_sus_methodB_admission4
- extract_sus_methodB_admission5
- extract_sus_methodC_admission1
- extract_sus_methodC_admission2
- extract_sus_methodC_admission3
- extract_sus_methodC_admission4
- extract_sus_methodC_admission5
outputs:
highly_sensitive:
rds: output/admissions/processed_sus*.rds
validation_events:
run: r:latest analysis/validation_events.R
needs:
- process_isaric
- process_sus
outputs:
moderately_sensitive:
csv: output/validation_events/*.csv
validation_characteristics:
run: r:latest analysis/validation_characteristics.R
needs:
- process_isaric
- process_sus
outputs:
moderately_sensitive:
csv: output/validation_characteristics/*.csv
jpg: output/validation_characteristics/*.jpg
## # # # # # # # # # # # # # # # # # # #
## End
## # # # # # # # # # # # # # # # # # # #