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project.yaml
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project.yaml
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################################################################################
#
# Description: This script defines the project pipeline - it specifys the
# execution orders for all the code in this repo using a series of
# actions.
#
# Author(s): M Green
# Date last updated: 07/08/2023
#
################################################################################
version: '3.0'
expectations:
population_size: 1000
actions:
# Extract isaric data ----
extract_first_isaric_admission:
run: >
ehrql:v0 generate-dataset analysis/dataset_definition_isaric.py
--output 'output/admissions/isaric_admission1.csv.gz'
outputs:
highly_sensitive:
csv: output/admissions/isaric_admission1.csv.gz
# Extract sus data ----
extract_sus_methodA_admission1_cohortextractor:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
--param admission_number=1
--param admission_method=A
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
extract_first_sus_admission_methodA_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodA_admission1_ehrQL.csv.gz
--
--admission_method A
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodA_admission1_ehrQL.csv.gz
extract_first_sus_admission_methodB_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodB_admission1_ehrQL.csv.gz
--
--admission_method B
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodB_admission1_ehrQL.csv.gz
extract_first_sus_admission_methodC_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodC_admission1_ehrQL.csv.gz
--
--admission_method C
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodC_admission1_ehrQL.csv.gz
# Data properties ----
data_properties:
run: >
r:latest
analysis/data_properties.R
output/admissions/isaric_admission1.csv.gz
output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
output/admissions/sus_methodA_admission1_ehrQL.csv.gz
output/data_properties
needs: [extract_first_isaric_admission, extract_sus_methodA_admission1_cohortextractor, extract_first_sus_admission_methodA_ehrQL]
outputs:
moderately_sensitive:
txt1: output/data_properties/*.txt