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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population_covid_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2020 --output-dir=output/cohorts
outputs:
highly_sensitive:
cohort: output/cohorts/input_covid_2020.csv
generate_study_population_general_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2019 --output-dir=output/cohorts
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_2019.csv
generate_study_population_general_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2020 --output-dir=output/cohorts
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_2020.csv
generate_study_population_pneumonia_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia_2019 --output-dir=output/cohorts
outputs:
highly_sensitive:
cohort: output/cohorts/input_pneumonia_2019.csv
reconcile_sick_note_spells_covid_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2020"
needs: [generate_study_population_covid_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_covid_2020_with_duration.csv
reconcile_sick_note_spells_general_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_general_2019"
needs: [generate_study_population_general_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_general_2019_with_duration.csv
reconcile_sick_note_spells_general_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_general_2020"
needs: [generate_study_population_general_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_general_2020_with_duration.csv
reconcile_sick_note_spells_pneumonia_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_pneumonia_2019"
needs: [generate_study_population_pneumonia_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_pneumonia_2019_with_duration.csv
# matching_2019:
# run: python:latest python analysis/match_running.py "input_general_2019" "_2019" "2019-02-01" --output-dir=output/cohorts
# needs: [generate_study_population_covid_2020, generate_study_population_general_2019]
# outputs:
# moderately_sensitive:
# matching_report: output/cohorts/matching_report_2019.txt
# highly_sensitive:
# matched_cohort: output/cohorts/matched_matches_2019.csv
# matching_2020:
# run: python:latest python analysis/match_running.py "input_general_2020" "_2020" "2020-02-01" --output-dir=output/cohorts
# needs: [generate_study_population_covid_2020, generate_study_population_general_2020]
# outputs:
# moderately_sensitive:
# matching_report: output/cohorts/matching_report_2020.txt
# highly_sensitive:
# matched_cohort: output/cohorts/matched_matches_2020.csv
covid_2020_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_2020" --output-dir=output/cohorts
needs: [generate_study_population_covid_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_covid_2020.dta
general_2019_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "general_2019" --output-dir=output/cohorts
needs: [generate_study_population_general_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_general_2019.dta
general_2020_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "general_2020" --output-dir=output/cohorts
needs: [generate_study_population_general_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_general_2020.dta
pneumonia_2019_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia_2019" --output-dir=output/cohorts
needs: [generate_study_population_pneumonia_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_pneumonia_2019.dta
covid_2020_rates:
run: stata-mp:latest analysis/100_cr_simple_rates.do "covid_2020" --output-dir=output/tabfig
needs: [covid_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_2020.csv
general_2019_rates:
run: stata-mp:latest analysis/100_cr_simple_rates.do "general_2019" --output-dir=output/tabfig
needs: [general_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_general_2019.csv
general_2020_rates:
run: stata-mp:latest analysis/100_cr_simple_rates.do "general_2020" --output-dir=output/tabfig
needs: [general_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_general_2020.csv
pneumonia_2019_rates:
run: stata-mp:latest analysis/100_cr_simple_rates.do "pneumonia_2019" --output-dir=output/tabfig
needs: [pneumonia_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_pneumonia_2019.csv
append_cohorts:
run: stata-mp:latest analysis/200_cr_data_management_matching.do --output-dir=output/cohorts
needs: [covid_2020_rates_cohort, pneumonia_2019_rates_cohort, general_2020_rates_cohort, general_2019_rates_cohort]
outputs:
moderately_sensitive:
log: output/cohorts/append_cohorts.txt
highly_sensitive:
dataset: output/cohorts/combined_covid_pneumonia.dta
dataset2: output/cohorts/combined_covid_general_2019.dta
dataset3: output/cohorts/combined_covid_general_2020.dta
cox_models:
run: stata-mp:latest analysis/201_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv
describe_duration:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/describe_duration.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [reconcile_sick_note_spells_covid_2020, reconcile_sick_note_spells_general_2019, reconcile_sick_note_spells_general_2020, reconcile_sick_note_spells_pneumonia_2019]
outputs:
moderately_sensitive:
notebook: output/describe_duration.html
table: output/tabfig/med_iqr_overall.csv
table2: output/tabfig/med_iqr_age_group.csv
table3: output/tabfig/med_iqr_sex.csv
table4: output/tabfig/med_iqr_ethnicity.csv
table5: output/tabfig/med_iqr_imd.csv
table6: output/tabfig/med_iqr_region.csv