generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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######################################
# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract cohort data
## Learning disability
generate_ld_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ld --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_ld_*.feather
## Autism
generate_autism_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_autism --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_autism_*.feather
## Serious Mental Illness
generate_smi_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_smi --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_smi_*.feather
## Care home
generate_care_home_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_care_home --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_care_home_*.feather
## Dementia
generate_dementia_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dementia --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_dementia_*.feather
## Ethnicity
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_ethnicity.feather
# Data processing
## Add ethnicity
join_ethnicity:
run: python:latest python analysis/python/scripts/join_ethnicity.py
needs: [generate_ld_cohort, generate_autism_cohort, generate_smi_cohort, generate_care_home_cohort, generate_dementia_cohort, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/data/input*.feather
# Generate measures data
## Learning disability
generate_measures_ld:
run: cohortextractor:latest generate_measures --study-definition study_definition_ld --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_ld_*.csv
## Autism
generate_measures_autism:
run: cohortextractor:latest generate_measures --study-definition study_definition_autism --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_autism_*.csv
## Serious Mental Illness
generate_measures_smi:
run: cohortextractor:latest generate_measures --study-definition study_definition_smi --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_smi_*.csv
## Care home
generate_measures_care_home:
run: cohortextractor:latest generate_measures --study-definition study_definition_care_home --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_care_home_*.csv
## Dementia
generate_measures_dementia:
run: cohortextractor:latest generate_measures --study-definition study_definition_dementia --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_dementia_*.csv
# # Patient to practice lookup
# generate_study_population_practice_count:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output/data
# outputs:
# highly_sensitive:
# cohort: output/data/input_practice_count.csv
#
#
# # Practice counts
# get_practice_count:
# run: python:latest python analysis/python/scripts/get_practice_count.py --output-dir=output/data
# needs: [generate_study_population_practice_count]
# outputs:
# moderately_sensitive:
# text: output/data/practice_count.json
#
# # Patient counts
# get_patient_count:
# run: python:latest python analysis/python/scripts/get_patients_counts.py --output-dir=output/data
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# text: output/data/patient_count.json
#
# Measures notebook
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/python/notebooks/antipsychotics_measures.ipynb --execute --to html --output-dir=/workspace/output/results --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures_ld]
outputs:
moderately_sensitive:
notebook: output/results/antipsychotics_measures.html
# Process data
data_process:
run: r:latest analysis/r/scripts/00_process_data.R
needs: [generate_ld_cohort, generate_measures_ld]
outputs:
moderately_sensitive:
data: output/data/data_processed.rds