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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
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
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
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
combine_ons:
run: r:latest analysis/combine_ons.R
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
data: output/ons/ethnic_group*.csv
data2: output/ons/ethnic_group_NA*.csv
data3: output/ons/data_check*.csv
ons_plot:
run: r:latest analysis/ons_plots.R
needs: [combine_ons]
outputs:
moderately_sensitive:
plot_na: output/ons/na_removed/ethnicity_*.png
# ## Only to be run locally
# generate_report:
# run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.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:
# notebook: output/draft_report_ethnicity.html
# local_simple_run:
# run: python:latest python analysis/local_simple_run.py
# outputs:
# moderately_sensitive:
# tables: output/from_jobserver/release_2022_11_18/made_locally/*.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
# combine_ons:
# run: r:latest analysis/combine_ons.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# data: output/ons/ethnic_group*.csv
# data2: output/ons/ethnic_group_NA*.csv
# data3: output/ons/data_check*.csv
# ons_plot:
# run: r:latest analysis/ons_plots.R
# needs: [combine_ons]
# outputs:
# moderately_sensitive:
# plot_na: output/ons/na_removed/ethnicity_*.png
# iqr:
# run: r:latest analysis/iqr.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# full: output/simplified_output/5_group/tables/range_fullset.csv
# registered: output/simplified_output/5_group/tables/range_registered.csv
# figures: output/simplified_output/5_group/figures/density*.svg
# ## Only to be run locally
# generate_report:
# run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.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:
# notebook: output/draft_report_ethnicity.html
# local_simple_run:
# run: python:latest python analysis/local_simple_run_sot.py
# outputs:
# moderately_sensitive:
# tables: output/released/*.csv
################## over time
time_tables:
run: r:latest analysis/time/times.R
needs: [generate_study_population_time]
outputs:
moderately_sensitive:
data: output/time/*.csv
plots: output/time/*.png