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 data ----
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input.csv
# Process data ----
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
data2: output/data/data_processed.rds
# Inclusion/exclusion flow chart ----
flow_chart:
run: r:latest analysis/flow_chart.R
needs: [data_process]
outputs:
moderately_sensitive:
data: output/data/flowchart.csv
# Data properties ----
data_properties:
run: r:latest analysis/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
# Data summaries ----
simple_summaries:
run: r:latest -e 'rmarkdown::render("analysis/simple_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [generate_study_population, data_process]
outputs:
moderately_sensitive:
html: output/markdown/simple_summaries.html
# Table 1 ----
table_1:
run: r:latest analysis/table_1.R
needs: [data_process]
outputs:
moderately_sensitive:
table: output/tables/table1*.html
# Table 2 ----
table_2:
run: r:latest analysis/table_2.R
needs: [data_process]
outputs:
moderately_sensitive:
table1: output/tables/table2.html
table2: output/tables/table2_redacted.html
table_ckd:
run: r:latest analysis/table_ckd.R
needs: [data_process]
outputs:
moderately_sensitive:
table1: output/tables/table_ckd.html
table2: output/tables/table_ckd_redacted.html
# Figure 1 ----
cummulative_incidence:
run: r:latest analysis/cumulative_incidence.R
needs: [data_process]
outputs:
moderately_sensitive:
data: output/data/surv_data*.csv
# Figure 2 ----
figure_2:
run: r:latest analysis/figure_2.R
needs: [data_process]
outputs:
moderately_sensitive:
png: output/figures/figure2*.png