generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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### CTV3, PRIMIS, SNOMED analysis
version: '3.0'
expectations:
population_size: 1000
actions:
split_codelist:
run: r:latest analysis/00_trim_snomed_codelist.r
outputs:
highly_sensitive:
data: codelists/ethnicity_*.csv
generate_study_population_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_5 --output-file output/extract_5/input_5.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_5/input_5.feather
# dataset report from reusable action https://github.com/opensafely-actions/dataset-report
generate_dataset_report_5:
run: >
dataset-report:v0.0.9
--input-files output/extract_5/input_5.feather
--output-dir output/extract_5
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
dataset_report: output/extract_5/input_5.html
generate_study_population_16:
run: cohortextractor:latest generate_cohort --study-definition study_definition_16 --output-file output/extract_16/input_16.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_16/input_16.feather
# dataset report from reusable action https://github.com/opensafely-actions/dataset-report
generate_dataset_report_16:
run: >
dataset-report:v0.0.9
--input-files output/extract_16/input_16.feather
--output-dir output/extract_16
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
dataset_report: output/extract_16/input_16.html
generate_study_population_time:
run: cohortextractor:latest generate_cohort --study-definition study_definition_time --output-file output/extract_time/input_time.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_time/input_time.feather
# dataset report from reusable action https://github.com/opensafely-actions/dataset-report
generate_dataset_report_time:
run: >
dataset-report:v0.0.9
--input-files output/extract_time/input_time.feather
--output-dir output/extract_time
needs: [generate_study_population_time]
outputs:
moderately_sensitive:
dataset_report: output/extract_time/input_time.html
execute_simple_validation_analyses:
run: python:latest python analysis/simple_validation_script.py
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
tables: output/simplified_output/5_group/tables/*.csv
execute_simple_validation_analyses_16:
run: python:latest python analysis/simple_validation_script_16.py
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
tables: output/simplified_output/16_group/tables/simpl*.csv
######## SUS
execute_simple_validation_analyses_sus:
run: python:latest python analysis/sus/simple_validation_script_sus.py
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
tables: output/sus/simplified_output/5_group/tables/*.csv
# figures: output/sus/simplified_output/5_group/figures/*.png
execute_simple_validation_analyses_16_sus:
run: python:latest python analysis/sus/simple_validation_script_16_sus.py
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
tables: output/sus/simplified_output/16_group/tables/simpl*.csv
report_tables:
run: python:latest python analysis/report_tables.py
needs: [execute_simple_validation_analyses_16_sus, execute_simple_validation_analyses_sus,execute_simple_validation_analyses,execute_simple_validation_analyses_16]
outputs:
moderately_sensitive:
tables: output/report_tables/*.csv
generate_ons_comparisons:
run: r:latest analysis/sus/combine_ons_sus.R
needs: [execute_simple_validation_analyses_16_sus,execute_simple_validation_analyses_sus]
outputs:
moderately_sensitive:
csvs: output/sus/simplified_output/*/tables/ethnic_group*.csv
##### draft report
generate_draft_report_rmd:
run: r:latest -e 'rmarkdown::render("notebooks_r/report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/report")'
needs: [generate_ons_comparisons,report_tables, execute_simple_validation_analyses,execute_simple_validation_analyses_16,execute_simple_validation_analyses_sus,execute_simple_validation_analyses_16_sus,generate_study_population_5]
outputs:
moderately_sensitive:
html: output/report/report.html
#### move released files to output/released
###### run locally for manuscript
##### local notebook
generate_local_runs:
run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/local_runs.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
outputs:
moderately_sensitive:
csvs: output/released/made_locally/*.csv
# process_ons_census_data:
# run: r:latest analysis/local/ons_process.R
# outputs:
# moderately_sensitive:
# csvs: data/*.csv.gz
# generate_local_ons_comparisons:
# run: r:latest analysis/local/combine_ons_sus.R
# needs: [process_ons_census_data]
# outputs:
# moderately_sensitive:
# csvs: output/released/made_locally/ethnic_group*.csv
# tests: output/tests/*.csv
## create outputs for the manuscript
## library(hrbrthemes) not currently available on the OS R image
# generate_manuscript_plots:
# run: r:latest analysis/local/local_manuscript_plots.R
# outputs:
# moderately_sensitive:
# plots: output/released/made_locally/*.png
## create outputs for the appendix
# `row_group.as_column = TRUE` option not currently available on the OS R image
# generate_appendix:
# run: r:latest analysis/local/appendix.R
# needs: [generate_local_runs]
# outputs:
# moderately_sensitive:
# html: output/released/made_locally/*.html
# pdf: output/released/made_locally/*.pdf