generated from opensafely/research-template
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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: 15/02/2022
#
################################################################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract data ----
extract_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/data/input.csv.gz
extract_stp_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_stp --output-dir=output/data --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/data/input_stp.csv.gz
extract_high_risk_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_high_risk --output-dir=output/data --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/data/input_high_risk.csv.gz
# Data processing ----
data_process:
run: r:latest analysis/process/process_data.R
needs: [extract_data]
outputs:
highly_sensitive:
data: output/data/data_processed*.rds
moderately_sensitive:
csv: output/coverage/n_excl_more_trtmnts_implausible_trtmnt_date.csv
data_process_high_risk:
run: r:latest analysis/process/process_data_high_risk.R
needs: [extract_high_risk_data]
outputs:
highly_sensitive:
data: output/data/data_processed_high_risk.rds
moderately_sensitive:
csv: output/data_properties/n_high_risk.csv
# Data summaries ----
data_properties:
run: r:latest analysis/descriptive/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
excl_crit_checks:
run: r:latest analysis/descriptive/excl_crit_checks.R
needs: [data_process]
outputs:
moderately_sensitive:
csv: output/data_properties/excl_crit.csv
# Sensitivity anslysis ----
sa_symptomatic_test:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/sa_symptomatic_test.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/coverage/sa_symptomatic_test.html
# Report ----
report_data:
run: r:latest analysis/descriptive/coverage_report_data.R
needs: [data_process]
outputs:
moderately_sensitive:
redacted_tables: output/coverage/table_*.csv
unredacted_tables: output/coverage/for-checks/table_*.csv
hosp_after_pos_test:
run: r:latest analysis/descriptive/discharge_adm_after_pos_test.R
needs: [data_process]
outputs:
moderately_sensitive:
redacted_table: output/coverage/table_admitted_after_pos_test.csv
# Variation by STP ----
stp_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/mabs-and-avs-by-stp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
needs: [data_process, extract_stp_data]
outputs:
moderately_sensitive:
html: output/variation/mabs-and-avs-by-stp.html
figures: output/variation/figure_*.csv
csvs: output/variation/table_*.csv
stp_decile_values_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/stp-decile-values.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
needs: [data_process, extract_stp_data]
outputs:
moderately_sensitive:
html: output/variation/stp-decile-values.html
csv1: output/variation/table_stp_coverage.csv
csv2: output/variation/stp_decile_values.csv
csv3: output/variation/stp_decile_values_weekly.csv
# Obs vs exp ----
obs_vs_exp_report:
run: r:latest -e 'rmarkdown::render("analysis/descriptive/obs-vs-exp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
needs: [data_process]
outputs:
moderately_sensitive:
html: output/variation/obs-vs-exp.html