generated from opensafely/research-template
/
project.yaml
72 lines (63 loc) · 2.56 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_acute_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_any_acute_covid_pri_care
outputs:
highly_sensitive:
cohort: output/input_any_acute_covid_pri_care.csv
generate_og_pc_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ongoing_post_covid
outputs:
highly_sensitive:
cohort: output/input_ongoing_post_covid.csv
generate_cohort_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all
outputs:
highly_sensitive:
cohort: output/input_all.csv
debug_cohorts:
run: r:latest analysis/debug_script.R
needs: [generate_acute_cohort, generate_og_pc_cohort, generate_cohort_all]
outputs:
moderately_sensitive:
debug_oc: output/debug_oc_counts.csv
debug_ac: output/debug_ac_counts.csv
debug_all_counts: output/debug_all_counts.csv
debug_all_crosstab: output/debug_all_diag_refer_crosstab.csv
debug_nuts_1_region: output/debug_nuts_1_region.csv
compliance_ratios:
run: r:latest analysis/guideline_compliance_ratios.R
needs: [generate_acute_cohort, generate_og_pc_cohort]
outputs:
moderately_sensitive:
pc_counts: output/ratios.csv
ref_rates: output/ref_rates_by_month.csv
descriptive_coding_script:
run: r:latest analysis/descriptive_coding_script.R
needs: [generate_cohort_all]
outputs:
moderately_sensitive:
Fig1: output/Fig_1.png
Fig1_numbers: output/Fig_1_numbers.csv
Fig2: output/Fig_2.png
Fig2_numbers: output/Fig_2_numbers.csv
Fig3: output/Fig_3.png
Fig3_numbers: output/Fig_3_numbers.csv
Table_1: output/Table_1.csv
Table_2: output/Table_2.csv
Table_3: output/Table_3.csv
HE_compliance_summary:
run: r:latest analysis/HE_compliance_summary.R
needs: [generate_acute_cohort]
outputs:
moderately_sensitive:
HE_summary_table_1_1: output/monthly_summary_tab_1_1.csv
HE_summary_fig_1_1_age: output/line_chart_1_1_age_group.png
HE_summary_fig_1_1_eth: output/line_chart_1_1_ethnicity.png
HE_summary_fig_1_1_IMD: output/line_chart_1_1_imd.png
HE_summary_fig_1_1_region: output/line_chart_1_1_region.png
HE_summary_fig_1_1_sex: output/line_chart_1_1_sex.png
HE_summary_fig_1_1_total: output/line_chart_1_1_total.png
HE_summary_table_1_8: output/monthly_summary_tab_1_8.csv