generated from opensafely/research-template
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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: 1000000
actions:
# Extract data for study population flow chart
generate_study_population_flow_chart_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
outputs:
highly_sensitive:
cohort: output/input_flow_chart.csv
# Calculate numbers for study population flow chart
flow_chart:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population_flow_chart_data]
outputs:
moderately_sensitive:
html: output/Study_definition_flow_chart.html
# Extract study data
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
# Process data
data_process_all:
run: r:latest analysis/R/Scripts/00_process_data.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
# Summarise data
data_properties_all:
run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process_all]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_all*.txt
# Practice ID summaries
practice_id:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries_practices.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
html: output/Data_summaries_practices.html
# Models
cox_models:
run: r:latest analysis/R/Scripts/02_Models.R
needs: [generate_study_population, data_process_all]
outputs:
highly_sensitive :
models: output/models/mod*.rds
# Models summaries
cox_models_summaries:
run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population, data_process_all, cox_models]
outputs:
moderately_sensitive:
html: output/Model_comparisons.html