generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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######################################
# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 10000
actions:
# Extract data ----
## Cohort data
generate_study_population_1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2018-01-01 to 2018-12-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_study_population_2:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2019-01-01 to 2019-12-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_study_population_3:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2020-01-01 to 2020-12-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/inpu*.csv
generate_study_population_4:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2021-01-01 to 2021-12-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/inp*.csv
generate_study_population_5:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2022-01-01 to 2022-03-01 by month"
--output-dir=output
--output-format=csv
outputs:
highly_sensitive:
cohort: output/in*.csv
## Ethnicity
generate_ethnicity_cohort:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv
# Data processing ----
## Add ethnicity
join_cohorts:
run: >
cohort-joiner:v0.0.48
--lhs output/input_*.csv
--rhs output/input_ethnicity.csv
--output-dir output/data
needs: [generate_study_population_1, generate_study_population_2,
generate_study_population_5, generate_study_population_3, generate_study_population_4,
generate_ethnicity_cohort]
outputs:
highly_sensitive:
cohort: output/data/input_*.csv
## Generate measures
generate_measures:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition
--output-dir output/data
needs: [join_cohorts]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_*.csv
## Process data - time series
process_data_ts:
run: r:latest analysis/process/process_data_ts.R
needs: [generate_measures, join_cohorts]
outputs:
moderately_sensitive:
measure_csv: output/joined/final_*.csv
## Process data - table
process_data_table:
run: r:latest analysis/process/process_data_table.R
needs: [generate_measures, join_cohorts]
outputs:
moderately_sensitive:
measure_csv: output/joined/final*.csv
# Results ---
## Time series
timeseries:
run: r:latest analysis/descriptive/time_series_stand.R
needs: [process_data_ts]
outputs:
moderately_sensitive:
table: output/time series/ts_*.csv
## Time series graphs
# graphs:
# run: r:latest analysis/descriptive/graphs.R
# needs: [timeseries]
# outputs:
# moderately_sensitive:
# plot: output/time series/graphs/graph*.png
## Table
table:
run: r:latest analysis/descriptive/table_stand.R
needs: [process_data_table]
outputs:
moderately_sensitive:
table: output/tables/table_*.csv