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project.yaml
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project.yaml
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version: "3.0"
expectations:
population_size: 50000
actions:
# Extract data required for matching for covid (all STPs)
extract_covid_matching:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_matching
outputs:
highly_sensitive:
cohort: output/input_covid_matching.csv
#Data management for covid_matching for matching with 2017 general population
clean_covid_matching_2017:
run: stata-mp:latest analysis/covid_matching_2017.do
needs: [extract_covid_matching]
outputs:
highly_sensitive:
analysis_dataset: output/covid_matching_2017.csv
moderately_sensitive:
log: logs/covid_matching_2017.log
#Extract data required for matching for 2017 (all STPs)
extract_2017_matching:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2017_matching
outputs:
highly_sensitive:
cohort: output/input_2017_matching.csv
#Data management for 2017_matching
clean_2017_matching:
run: stata-mp:latest analysis/2017_matching.do
needs: [extract_2017_matching, clean_covid_matching_2017]
outputs:
highly_sensitive:
analysis_dataset: output/2017_matching.csv
moderately_sensitive:
log: logs/2017_matching.log
# Split covid_matching_2017 and 2017_matching by STP
split_stps_2017:
run: stata-mp:latest analysis/split_stps_2017.do
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching]
outputs:
highly_sensitive:
covid_stp5: output/input_covid_matching_2017_stp5.csv
covid_stp6: output/input_covid_matching_2017_stp6.csv
covid_stp7: output/input_covid_matching_2017_stp7.csv
covid_stp8: output/input_covid_matching_2017_stp8.csv
covid_stp9: output/input_covid_matching_2017_stp9.csv
covid_stp10: output/input_covid_matching_2017_stp10.csv
covid_stp12: output/input_covid_matching_2017_stp12.csv
covid_stp13: output/input_covid_matching_2017_stp13.csv
covid_stp14: output/input_covid_matching_2017_stp14.csv
covid_stp15: output/input_covid_matching_2017_stp15.csv
covid_stp16: output/input_covid_matching_2017_stp16.csv
covid_stp17: output/input_covid_matching_2017_stp17.csv
covid_stp20: output/input_covid_matching_2017_stp20.csv
covid_stp21: output/input_covid_matching_2017_stp21.csv
covid_stp22: output/input_covid_matching_2017_stp22.csv
covid_stp23: output/input_covid_matching_2017_stp23.csv
covid_stp24: output/input_covid_matching_2017_stp24.csv
covid_stp25: output/input_covid_matching_2017_stp25.csv
covid_stp26: output/input_covid_matching_2017_stp26.csv
covid_stp27: output/input_covid_matching_2017_stp27.csv
covid_stp29: output/input_covid_matching_2017_stp29.csv
covid_stp33: output/input_covid_matching_2017_stp33.csv
covid_stp35: output/input_covid_matching_2017_stp35.csv
covid_stp36: output/input_covid_matching_2017_stp36.csv
covid_stp37: output/input_covid_matching_2017_stp37.csv
covid_stp40: output/input_covid_matching_2017_stp40.csv
covid_stp41: output/input_covid_matching_2017_stp41.csv
covid_stp42: output/input_covid_matching_2017_stp42.csv
covid_stp43: output/input_covid_matching_2017_stp43.csv
covid_stp44: output/input_covid_matching_2017_stp44.csv
covid_stp49: output/input_covid_matching_2017_stp49.csv
2017_stp5: output/input_2017_matching_stp5.csv
2017_stp6: output/input_2017_matching_stp6.csv
2017_stp7: output/input_2017_matching_stp7.csv
2017_stp8: output/input_2017_matching_stp8.csv
2017_stp9: output/input_2017_matching_stp9.csv
2017_stp10: output/input_2017_matching_stp10.csv
2017_stp12: output/input_2017_matching_stp12.csv
2017_stp13: output/input_2017_matching_stp13.csv
2017_stp14: output/input_2017_matching_stp14.csv
2017_stp15: output/input_2017_matching_stp15.csv
2017_stp16: output/input_2017_matching_stp16.csv
2017_stp17: output/input_2017_matching_stp17.csv
2017_stp20: output/input_2017_matching_stp20.csv
2017_stp21: output/input_2017_matching_stp21.csv
2017_stp22: output/input_2017_matching_stp22.csv
2017_stp23: output/input_2017_matching_stp23.csv
2017_stp24: output/input_2017_matching_stp24.csv
2017_stp25: output/input_2017_matching_stp25.csv
2017_stp26: output/input_2017_matching_stp26.csv
2017_stp27: output/input_2017_matching_stp27.csv
2017_stp29: output/input_2017_matching_stp29.csv
2017_stp33: output/input_2017_matching_stp33.csv
2017_stp35: output/input_2017_matching_stp35.csv
2017_stp36: output/input_2017_matching_stp36.csv
2017_stp37: output/input_2017_matching_stp37.csv
2017_stp40: output/input_2017_matching_stp40.csv
2017_stp41: output/input_2017_matching_stp41.csv
2017_stp42: output/input_2017_matching_stp42.csv
2017_stp43: output/input_2017_matching_stp43.csv
2017_stp44: output/input_2017_matching_stp44.csv
2017_stp49: output/input_2017_matching_stp49.csv
moderately_sensitive:
log: logs/split_stps_2017.log
match_2017_stp5:
run: python:latest python analysis/match_2017_stp5.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp5: output/matching_report_2017_stp5.txt
highly_sensitive:
matched_matches_stp5: output/matched_matches_2017_stp5.csv
matched_cases_stp5: output/matched_cases_2017_stp5.csv
matched_all_stp5: output/matched_combined_2017_stp5.csv
match_2017_stp6:
run: python:latest python analysis/match_2017_stp6.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp6: output/matching_report_2017_stp6.txt
highly_sensitive:
matched_matches_stp6: output/matched_matches_2017_stp6.csv
matched_cases_stp6: output/matched_cases_2017_stp6.csv
matched_all_stp6: output/matched_combined_2017_stp6.csv
match_2017_stp7:
run: python:latest python analysis/match_2017_stp7.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp7: output/matching_report_2017_stp7.txt
highly_sensitive:
matched_matches_stp7: output/matched_matches_2017_stp7.csv
matched_cases_stp7: output/matched_cases_2017_stp7.csv
matched_all_stp7: output/matched_combined_2017_stp7.csv
match_2017_stp8:
run: python:latest python analysis/match_2017_stp8.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp8: output/matching_report_2017_stp8.txt
highly_sensitive:
matched_matches_stp8: output/matched_matches_2017_stp8.csv
matched_cases_stp8: output/matched_cases_2017_stp8.csv
matched_all_stp8: output/matched_combined_2017_stp8.csv
match_2017_stp9:
run: python:latest python analysis/match_2017_stp9.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp9: output/matching_report_2017_stp9.txt
highly_sensitive:
matched_matches_stp9: output/matched_matches_2017_stp9.csv
matched_cases_stp9: output/matched_cases_2017_stp9.csv
matched_all_stp9: output/matched_combined_2017_stp9.csv
match_2017_stp10:
run: python:latest python analysis/match_2017_stp10.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp10: output/matching_report_2017_stp10.txt
highly_sensitive:
matched_matches_stp10: output/matched_matches_2017_stp10.csv
matched_cases_stp10: output/matched_cases_2017_stp10.csv
matched_all_stp10: output/matched_combined_2017_stp10.csv
match_2017_stp12:
run: python:latest python analysis/match_2017_stp12.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp12: output/matching_report_2017_stp12.txt
highly_sensitive:
matched_matches_stp12: output/matched_matches_2017_stp12.csv
matched_cases_stp12: output/matched_cases_2017_stp12.csv
matched_all_stp12: output/matched_combined_2017_stp12.csv
match_2017_stp13:
run: python:latest python analysis/match_2017_stp13.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp13: output/matching_report_2017_stp13.txt
highly_sensitive:
matched_matches_stp13: output/matched_matches_2017_stp13.csv
matched_cases_stp13: output/matched_cases_2017_stp13.csv
matched_all_stp13: output/matched_combined_2017_stp13.csv
match_2017_stp14:
run: python:latest python analysis/match_2017_stp14.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp14: output/matching_report_2017_stp14.txt
highly_sensitive:
matched_matches_stp14: output/matched_matches_2017_stp14.csv
matched_cases_stp14: output/matched_cases_2017_stp14.csv
matched_all_stp14: output/matched_combined_2017_stp14.csv
match_2017_stp15:
run: python:latest python analysis/match_2017_stp15.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp15: output/matching_report_2017_stp15.txt
highly_sensitive:
matched_matches_stp15: output/matched_matches_2017_stp15.csv
matched_cases_stp15: output/matched_cases_2017_stp15.csv
matched_all_stp15: output/matched_combined_2017_stp15.csv
match_2017_stp16:
run: python:latest python analysis/match_2017_stp16.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp16: output/matching_report_2017_stp16.txt
highly_sensitive:
matched_matches_stp16: output/matched_matches_2017_stp16.csv
matched_cases_stp16: output/matched_cases_2017_stp16.csv
matched_all_stp16: output/matched_combined_2017_stp16.csv
match_2017_stp17:
run: python:latest python analysis/match_2017_stp17.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp17: output/matching_report_2017_stp17.txt
highly_sensitive:
matched_matches_stp17: output/matched_matches_2017_stp17.csv
matched_cases_stp17: output/matched_cases_2017_stp17.csv
matched_all_stp17: output/matched_combined_2017_stp17.csv
match_2017_stp20:
run: python:latest python analysis/match_2017_stp20.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp20: output/matching_report_2017_stp20.txt
highly_sensitive:
matched_matches_stp20: output/matched_matches_2017_stp20.csv
matched_cases_stp20: output/matched_cases_2017_stp20.csv
matched_all_stp20: output/matched_combined_2017_stp20.csv
match_2017_stp21:
run: python:latest python analysis/match_2017_stp21.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp21: output/matching_report_2017_stp21.txt
highly_sensitive:
matched_matches_stp21: output/matched_matches_2017_stp21.csv
matched_cases_stp21: output/matched_cases_2017_stp21.csv
matched_all_stp21: output/matched_combined_2017_stp21.csv
match_2017_stp22:
run: python:latest python analysis/match_2017_stp22.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp22: output/matching_report_2017_stp22.txt
highly_sensitive:
matched_matches_stp22: output/matched_matches_2017_stp22.csv
matched_cases_stp22: output/matched_cases_2017_stp22.csv
matched_all_stp22: output/matched_combined_2017_stp22.csv
match_2017_stp23:
run: python:latest python analysis/match_2017_stp23.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp23: output/matching_report_2017_stp23.txt
highly_sensitive:
matched_matches_stp23: output/matched_matches_2017_stp23.csv
matched_cases_stp23: output/matched_cases_2017_stp23.csv
matched_all_stp23: output/matched_combined_2017_stp23.csv
match_2017_stp24:
run: python:latest python analysis/match_2017_stp24.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp24: output/matching_report_2017_stp24.txt
highly_sensitive:
matched_matches_stp24: output/matched_matches_2017_stp24.csv
matched_cases_stp24: output/matched_cases_2017_stp24.csv
matched_all_stp24: output/matched_combined_2017_stp24.csv
match_2017_stp25:
run: python:latest python analysis/match_2017_stp25.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp25: output/matching_report_2017_stp25.txt
highly_sensitive:
matched_matches_stp25: output/matched_matches_2017_stp25.csv
matched_cases_stp25: output/matched_cases_2017_stp25.csv
matched_all_stp25: output/matched_combined_2017_stp25.csv
match_2017_stp26:
run: python:latest python analysis/match_2017_stp26.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp26: output/matching_report_2017_stp26.txt
highly_sensitive:
matched_matches_stp26: output/matched_matches_2017_stp26.csv
matched_cases_stp26: output/matched_cases_2017_stp26.csv
matched_all_stp26: output/matched_combined_2017_stp26.csv
match_2017_stp27:
run: python:latest python analysis/match_2017_stp27.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp27: output/matching_report_2017_stp27.txt
highly_sensitive:
matched_matches_stp27: output/matched_matches_2017_stp27.csv
matched_cases_stp27: output/matched_cases_2017_stp27.csv
matched_all_stp27: output/matched_combined_2017_stp27.csv
match_2017_stp29:
run: python:latest python analysis/match_2017_stp29.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp29: output/matching_report_2017_stp29.txt
highly_sensitive:
matched_matches_stp29: output/matched_matches_2017_stp29.csv
matched_cases_stp29: output/matched_cases_2017_stp29.csv
matched_all_stp29: output/matched_combined_2017_stp29.csv
match_2017_stp33:
run: python:latest python analysis/match_2017_stp33.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp33: output/matching_report_2017_stp33.txt
highly_sensitive:
matched_matches_stp33: output/matched_matches_2017_stp33.csv
matched_cases_stp33: output/matched_cases_2017_stp33.csv
matched_all_stp33: output/matched_combined_2017_stp33.csv
match_2017_stp35:
run: python:latest python analysis/match_2017_stp35.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp35: output/matching_report_2017_stp35.txt
highly_sensitive:
matched_matches_stp35: output/matched_matches_2017_stp35.csv
matched_cases_stp35: output/matched_cases_2017_stp35.csv
matched_all_stp35: output/matched_combined_2017_stp35.csv
match_2017_stp36:
run: python:latest python analysis/match_2017_stp36.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp36: output/matching_report_2017_stp36.txt
highly_sensitive:
matched_matches_stp36: output/matched_matches_2017_stp36.csv
matched_cases_stp36: output/matched_cases_2017_stp36.csv
matched_all_stp36: output/matched_combined_2017_stp36.csv
match_2017_stp37:
run: python:latest python analysis/match_2017_stp37.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp37: output/matching_report_2017_stp37.txt
highly_sensitive:
matched_matches_stp37: output/matched_matches_2017_stp37.csv
matched_cases_stp37: output/matched_cases_2017_stp37.csv
matched_all_stp37: output/matched_combined_2017_stp37.csv
match_2017_stp40:
run: python:latest python analysis/match_2017_stp40.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp40: output/matching_report_2017_stp40.txt
highly_sensitive:
matched_matches_stp40: output/matched_matches_2017_stp40.csv
matched_cases_stp40: output/matched_cases_2017_stp40.csv
matched_all_stp40: output/matched_combined_2017_stp40.csv
match_2017_stp41:
run: python:latest python analysis/match_2017_stp41.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp41: output/matching_report_2017_stp41.txt
highly_sensitive:
matched_matches_stp41: output/matched_matches_2017_stp41.csv
matched_cases_stp41: output/matched_cases_2017_stp41.csv
matched_all_stp41: output/matched_combined_2017_stp41.csv
match_2017_stp42:
run: python:latest python analysis/match_2017_stp42.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp42: output/matching_report_2017_stp42.txt
highly_sensitive:
matched_matches_stp42: output/matched_matches_2017_stp42.csv
matched_cases_stp42: output/matched_cases_2017_stp42.csv
matched_all_stp42: output/matched_combined_2017_stp42.csv
match_2017_stp43:
run: python:latest python analysis/match_2017_stp43.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp43: output/matching_report_2017_stp43.txt
highly_sensitive:
matched_matches_stp43: output/matched_matches_2017_stp43.csv
matched_cases_stp43: output/matched_cases_2017_stp43.csv
matched_all_stp43: output/matched_combined_2017_stp43.csv
match_2017_stp44:
run: python:latest python analysis/match_2017_stp44.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp44: output/matching_report_2017_stp44.txt
highly_sensitive:
matched_matches_stp44: output/matched_matches_2017_stp44.csv
matched_cases_stp44: output/matched_cases_2017_stp44.csv
matched_all_stp44: output/matched_combined_2017_stp44.csv
match_2017_stp49:
run: python:latest python analysis/match_2017_stp49.py
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017]
outputs:
moderately_sensitive:
matching_report_stp49: output/matching_report_2017_stp49.txt
highly_sensitive:
matched_matches_stp49: output/matched_matches_2017_stp49.csv
matched_cases_stp49: output/matched_cases_2017_stp49.csv
matched_all_stp49: output/matched_combined_2017_stp49.csv
combine_stps_covid_2017:
run: stata-mp:latest analysis/combine_stps_covid_2017.do
needs: [match_2017_stp5, match_2017_stp6, match_2017_stp7, match_2017_stp8, match_2017_stp9,
match_2017_stp10, match_2017_stp12, match_2017_stp13, match_2017_stp14, match_2017_stp15,
match_2017_stp16, match_2017_stp17, match_2017_stp20, match_2017_stp21, match_2017_stp22,
match_2017_stp23, match_2017_stp24, match_2017_stp25, match_2017_stp26, match_2017_stp27,
match_2017_stp29, match_2017_stp33, match_2017_stp35, match_2017_stp36, match_2017_stp37,
match_2017_stp40, match_2017_stp41, match_2017_stp42, match_2017_stp43, match_2017_stp44,
match_2017_stp49]
outputs:
highly_sensitive:
matched_cases_combined: output/input_combined_stps_covid_2017.csv
moderately_sensitive:
log: logs/combine_stps_covid_2017.log
combine_stps_matches_2017:
run: stata-mp:latest analysis/combine_stps_matches_2017.do
needs: [match_2017_stp5, match_2017_stp6, match_2017_stp7, match_2017_stp8, match_2017_stp9,
match_2017_stp10, match_2017_stp12, match_2017_stp13, match_2017_stp14, match_2017_stp15,
match_2017_stp16, match_2017_stp17, match_2017_stp20, match_2017_stp21, match_2017_stp22,
match_2017_stp23, match_2017_stp24, match_2017_stp25, match_2017_stp26, match_2017_stp27,
match_2017_stp29, match_2017_stp33, match_2017_stp35, match_2017_stp36, match_2017_stp37,
match_2017_stp40, match_2017_stp41, match_2017_stp42, match_2017_stp43, match_2017_stp44,
match_2017_stp49]
outputs:
highly_sensitive:
matched_matches_combined: output/input_combined_stps_matches_2017.csv
moderately_sensitive:
log: logs/combine_stps_matches_2017.log
extract_covid_2017_additional:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2017_additional
needs: [combine_stps_covid_2017]
outputs:
highly_sensitive:
cohort: output/input_covid_2017_additional.csv
extract_2017_additional:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2017_additional
needs: [combine_stps_matches_2017]
outputs:
highly_sensitive:
cohort: output/input_2017_additional.csv
analysis_2017:
run: stata-mp:latest analysis/analysis_2017.do
needs: [extract_covid_matching, clean_covid_matching_2017, extract_2017_matching, clean_2017_matching, split_stps_2017, match_2017_stp5, match_2017_stp6, match_2017_stp7, match_2017_stp8, match_2017_stp9, match_2017_stp10, match_2017_stp12, match_2017_stp13, match_2017_stp14, match_2017_stp15, match_2017_stp16, match_2017_stp17, match_2017_stp20, match_2017_stp21, match_2017_stp22, match_2017_stp23, match_2017_stp24, match_2017_stp25, match_2017_stp26, match_2017_stp27, match_2017_stp29, match_2017_stp33, match_2017_stp35, match_2017_stp36, match_2017_stp37, match_2017_stp40, match_2017_stp41, match_2017_stp42, match_2017_stp43, match_2017_stp44, match_2017_stp49, combine_stps_covid_2017, combine_stps_matches_2017, extract_covid_2017_additional, extract_2017_additional]
outputs:
highly_sensitive:
analysis: output/analysis_2017.dta
moderately_sensitive:
log: logs/analysis_2017.log
extract_covid_hospitalised:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_hospitalised
outputs:
highly_sensitive:
cohort: output/input_covid_hospitalised.csv
extract_pneumonia_hospitalised:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia_hospitalised
outputs:
highly_sensitive:
cohort: output/input_pneumonia_hospitalised.csv
analysis_hospitalised:
run: stata-mp:latest analysis/analysis_hospitalised.do
needs: [extract_covid_hospitalised, extract_pneumonia_hospitalised]
outputs:
highly_sensitive:
analysis: output/analysis_hospitalised.dta
moderately_sensitive:
log: logs/analysis_hospitalised.log
#Data management for covid_matching for matching with 2020 general population
clean_covid_matching_2020:
run: stata-mp:latest analysis/covid_matching_2020.do
needs: [extract_asthma_matching_2020]
outputs:
highly_sensitive:
analysis_dataset: output/covid_matching_2020.csv
moderately_sensitive:
log: logs/covid_matching_2020.log
#Extract data required for matching for 2020 (all STPs)
extract_2020_matching:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2020_matching
outputs:
highly_sensitive:
cohort: output/input_2020_matching.csv
#Data management for 2020_matching
clean_2020_matching:
run: stata-mp:latest analysis/2020_matching.do
needs: [extract_2020_matching_asthma, clean_covid_matching_2020]
outputs:
highly_sensitive:
analysis_dataset: output/2020_matching.csv
moderately_sensitive:
log: logs/2020_matching.log
# Split covid_matching_2020 and 2020_matching by STP
split_stps_2020:
run: stata-mp:latest analysis/split_stps_2020.do
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching]
outputs:
highly_sensitive:
covid_stp5: output/input_covid_matching_2020_stp5.csv
covid_stp6: output/input_covid_matching_2020_stp6.csv
covid_stp7: output/input_covid_matching_2020_stp7.csv
covid_stp8: output/input_covid_matching_2020_stp8.csv
covid_stp9: output/input_covid_matching_2020_stp9.csv
covid_stp10: output/input_covid_matching_2020_stp10.csv
covid_stp12: output/input_covid_matching_2020_stp12.csv
covid_stp13: output/input_covid_matching_2020_stp13.csv
covid_stp14: output/input_covid_matching_2020_stp14.csv
covid_stp15: output/input_covid_matching_2020_stp15.csv
covid_stp16: output/input_covid_matching_2020_stp16.csv
covid_stp17: output/input_covid_matching_2020_stp17.csv
covid_stp20: output/input_covid_matching_2020_stp20.csv
covid_stp21: output/input_covid_matching_2020_stp21.csv
covid_stp22: output/input_covid_matching_2020_stp22.csv
covid_stp23: output/input_covid_matching_2020_stp23.csv
covid_stp24: output/input_covid_matching_2020_stp24.csv
covid_stp25: output/input_covid_matching_2020_stp25.csv
covid_stp26: output/input_covid_matching_2020_stp26.csv
covid_stp27: output/input_covid_matching_2020_stp27.csv
covid_stp29: output/input_covid_matching_2020_stp29.csv
covid_stp33: output/input_covid_matching_2020_stp33.csv
covid_stp35: output/input_covid_matching_2020_stp35.csv
covid_stp36: output/input_covid_matching_2020_stp36.csv
covid_stp37: output/input_covid_matching_2020_stp37.csv
covid_stp40: output/input_covid_matching_2020_stp40.csv
covid_stp41: output/input_covid_matching_2020_stp41.csv
covid_stp42: output/input_covid_matching_2020_stp42.csv
covid_stp43: output/input_covid_matching_2020_stp43.csv
covid_stp44: output/input_covid_matching_2020_stp44.csv
covid_stp49: output/input_covid_matching_2020_stp49.csv
2020_stp5: output/input_2020_matching_stp5.csv
2020_stp6: output/input_2020_matching_stp6.csv
2020_stp7: output/input_2020_matching_stp7.csv
2020_stp8: output/input_2020_matching_stp8.csv
2020_stp9: output/input_2020_matching_stp9.csv
2020_stp10: output/input_2020_matching_stp10.csv
2020_stp12: output/input_2020_matching_stp12.csv
2020_stp13: output/input_2020_matching_stp13.csv
2020_stp14: output/input_2020_matching_stp14.csv
2020_stp15: output/input_2020_matching_stp15.csv
2020_stp16: output/input_2020_matching_stp16.csv
2020_stp17: output/input_2020_matching_stp17.csv
2020_stp20: output/input_2020_matching_stp20.csv
2020_stp21: output/input_2020_matching_stp21.csv
2020_stp22: output/input_2020_matching_stp22.csv
2020_stp23: output/input_2020_matching_stp23.csv
2020_stp24: output/input_2020_matching_stp24.csv
2020_stp25: output/input_2020_matching_stp25.csv
2020_stp26: output/input_2020_matching_stp26.csv
2020_stp27: output/input_2020_matching_stp27.csv
2020_stp29: output/input_2020_matching_stp29.csv
2020_stp33: output/input_2020_matching_stp33.csv
2020_stp35: output/input_2020_matching_stp35.csv
2020_stp36: output/input_2020_matching_stp36.csv
2020_stp37: output/input_2020_matching_stp37.csv
2020_stp40: output/input_2020_matching_stp40.csv
2020_stp41: output/input_2020_matching_stp41.csv
2020_stp42: output/input_2020_matching_stp42.csv
2020_stp43: output/input_2020_matching_stp43.csv
2020_stp44: output/input_2020_matching_stp44.csv
2020_stp49: output/input_2020_matching_stp49.csv
moderately_sensitive:
log: logs/split_stps_2020.log
match_2020_stp5:
run: python:latest python analysis/match_2020_stp5.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp5: output/matching_report_2020_stp5.txt
highly_sensitive:
matched_matches_stp5: output/matched_matches_2020_stp5.csv
matched_cases_stp5: output/matched_cases_2020_stp5.csv
matched_all_stp5: output/matched_combined_2020_stp5.csv
match_2020_stp6:
run: python:latest python analysis/match_2020_stp6.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp6: output/matching_report_2020_stp6.txt
highly_sensitive:
matched_matches_stp6: output/matched_matches_2020_stp6.csv
matched_cases_stp6: output/matched_cases_2020_stp6.csv
matched_all_stp6: output/matched_combined_2020_stp6.csv
match_2020_stp7:
run: python:latest python analysis/match_2020_stp7.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp7: output/matching_report_2020_stp7.txt
highly_sensitive:
matched_matches_stp7: output/matched_matches_2020_stp7.csv
matched_cases_stp7: output/matched_cases_2020_stp7.csv
matched_all_stp7: output/matched_combined_2020_stp7.csv
match_2020_stp8:
run: python:latest python analysis/match_2020_stp8.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp8: output/matching_report_2020_stp8.txt
highly_sensitive:
matched_matches_stp8: output/matched_matches_2020_stp8.csv
matched_cases_stp8: output/matched_cases_2020_stp8.csv
matched_all_stp8: output/matched_combined_2020_stp8.csv
match_2020_stp9:
run: python:latest python analysis/match_2020_stp9.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp9: output/matching_report_2020_stp9.txt
highly_sensitive:
matched_matches_stp9: output/matched_matches_2020_stp9.csv
matched_cases_stp9: output/matched_cases_2020_stp9.csv
matched_all_stp9: output/matched_combined_2020_stp9.csv
match_2020_stp10:
run: python:latest python analysis/match_2020_stp10.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp10: output/matching_report_2020_stp10.txt
highly_sensitive:
matched_matches_stp10: output/matched_matches_2020_stp10.csv
matched_cases_stp10: output/matched_cases_2020_stp10.csv
matched_all_stp10: output/matched_combined_2020_stp10.csv
match_2020_stp12:
run: python:latest python analysis/match_2020_stp12.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp12: output/matching_report_2020_stp12.txt
highly_sensitive:
matched_matches_stp12: output/matched_matches_2020_stp12.csv
matched_cases_stp12: output/matched_cases_2020_stp12.csv
matched_all_stp12: output/matched_combined_2020_stp12.csv
match_2020_stp13:
run: python:latest python analysis/match_2020_stp13.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp13: output/matching_report_2020_stp13.txt
highly_sensitive:
matched_matches_stp13: output/matched_matches_2020_stp13.csv
matched_cases_stp13: output/matched_cases_2020_stp13.csv
matched_all_stp13: output/matched_combined_2020_stp13.csv
match_2020_stp14:
run: python:latest python analysis/match_2020_stp14.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp14: output/matching_report_2020_stp14.txt
highly_sensitive:
matched_matches_stp14: output/matched_matches_2020_stp14.csv
matched_cases_stp14: output/matched_cases_2020_stp14.csv
matched_all_stp14: output/matched_combined_2020_stp14.csv
match_2020_stp15:
run: python:latest python analysis/match_2020_stp15.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp15: output/matching_report_2020_stp15.txt
highly_sensitive:
matched_matches_stp15: output/matched_matches_2020_stp15.csv
matched_cases_stp15: output/matched_cases_2020_stp15.csv
matched_all_stp15: output/matched_combined_2020_stp15.csv
match_2020_stp16:
run: python:latest python analysis/match_2020_stp16.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp16: output/matching_report_2020_stp16.txt
highly_sensitive:
matched_matches_stp16: output/matched_matches_2020_stp16.csv
matched_cases_stp16: output/matched_cases_2020_stp16.csv
matched_all_stp16: output/matched_combined_2020_stp16.csv
match_2020_stp17:
run: python:latest python analysis/match_2020_stp17.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp17: output/matching_report_2020_stp17.txt
highly_sensitive:
matched_matches_stp17: output/matched_matches_2020_stp17.csv
matched_cases_stp17: output/matched_cases_2020_stp17.csv
matched_all_stp17: output/matched_combined_2020_stp17.csv
match_2020_stp20:
run: python:latest python analysis/match_2020_stp20.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp20: output/matching_report_2020_stp20.txt
highly_sensitive:
matched_matches_stp20: output/matched_matches_2020_stp20.csv
matched_cases_stp20: output/matched_cases_2020_stp20.csv
matched_all_stp20: output/matched_combined_2020_stp20.csv
match_2020_stp21:
run: python:latest python analysis/match_2020_stp21.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp21: output/matching_report_2020_stp21.txt
highly_sensitive:
matched_matches_stp21: output/matched_matches_2020_stp21.csv
matched_cases_stp21: output/matched_cases_2020_stp21.csv
matched_all_stp21: output/matched_combined_2020_stp21.csv
match_2020_stp22:
run: python:latest python analysis/match_2020_stp22.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp22: output/matching_report_2020_stp22.txt
highly_sensitive:
matched_matches_stp22: output/matched_matches_2020_stp22.csv
matched_cases_stp22: output/matched_cases_2020_stp22.csv
matched_all_stp22: output/matched_combined_2020_stp22.csv
match_2020_stp23:
run: python:latest python analysis/match_2020_stp23.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp23: output/matching_report_2020_stp23.txt
highly_sensitive:
matched_matches_stp23: output/matched_matches_2020_stp23.csv
matched_cases_stp23: output/matched_cases_2020_stp23.csv
matched_all_stp23: output/matched_combined_2020_stp23.csv
match_2020_stp24:
run: python:latest python analysis/match_2020_stp24.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp24: output/matching_report_2020_stp24.txt
highly_sensitive:
matched_matches_stp24: output/matched_matches_2020_stp24.csv
matched_cases_stp24: output/matched_cases_2020_stp24.csv
matched_all_stp24: output/matched_combined_2020_stp24.csv
match_2020_stp25:
run: python:latest python analysis/match_2020_stp25.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp25: output/matching_report_2020_stp25.txt
highly_sensitive:
matched_matches_stp25: output/matched_matches_2020_stp25.csv
matched_cases_stp25: output/matched_cases_2020_stp25.csv
matched_all_stp25: output/matched_combined_2020_stp25.csv
match_2020_stp26:
run: python:latest python analysis/match_2020_stp26.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp26: output/matching_report_2020_stp26.txt
highly_sensitive:
matched_matches_stp26: output/matched_matches_2020_stp26.csv
matched_cases_stp26: output/matched_cases_2020_stp26.csv
matched_all_stp26: output/matched_combined_2020_stp26.csv
match_2020_stp27:
run: python:latest python analysis/match_2020_stp27.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp27: output/matching_report_2020_stp27.txt
highly_sensitive:
matched_matches_stp27: output/matched_matches_2020_stp27.csv
matched_cases_stp27: output/matched_cases_2020_stp27.csv
matched_all_stp27: output/matched_combined_2020_stp27.csv
match_2020_stp29:
run: python:latest python analysis/match_2020_stp29.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp29: output/matching_report_2020_stp29.txt
highly_sensitive:
matched_matches_stp29: output/matched_matches_2020_stp29.csv
matched_cases_stp29: output/matched_cases_2020_stp29.csv
matched_all_stp29: output/matched_combined_2020_stp29.csv
match_2020_stp33:
run: python:latest python analysis/match_2020_stp33.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp33: output/matching_report_2020_stp33.txt
highly_sensitive:
matched_matches_stp33: output/matched_matches_2020_stp33.csv
matched_cases_stp33: output/matched_cases_2020_stp33.csv
matched_all_stp33: output/matched_combined_2020_stp33.csv
match_2020_stp35:
run: python:latest python analysis/match_2020_stp35.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp35: output/matching_report_2020_stp35.txt
highly_sensitive:
matched_matches_stp35: output/matched_matches_2020_stp35.csv
matched_cases_stp35: output/matched_cases_2020_stp35.csv
matched_all_stp35: output/matched_combined_2020_stp35.csv
match_2020_stp36:
run: python:latest python analysis/match_2020_stp36.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp36: output/matching_report_2020_stp36.txt
highly_sensitive:
matched_matches_stp36: output/matched_matches_2020_stp36.csv
matched_cases_stp36: output/matched_cases_2020_stp36.csv
matched_all_stp36: output/matched_combined_2020_stp36.csv
match_2020_stp37:
run: python:latest python analysis/match_2020_stp37.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp37: output/matching_report_2020_stp37.txt
highly_sensitive:
matched_matches_stp37: output/matched_matches_2020_stp37.csv
matched_cases_stp37: output/matched_cases_2020_stp37.csv
matched_all_stp37: output/matched_combined_2020_stp37.csv
match_2020_stp40:
run: python:latest python analysis/match_2020_stp40.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp40: output/matching_report_2020_stp40.txt
highly_sensitive:
matched_matches_stp40: output/matched_matches_2020_stp40.csv
matched_cases_stp40: output/matched_cases_2020_stp40.csv
matched_all_stp40: output/matched_combined_2020_stp40.csv
match_2020_stp41:
run: python:latest python analysis/match_2020_stp41.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp41: output/matching_report_2020_stp41.txt
highly_sensitive:
matched_matches_stp41: output/matched_matches_2020_stp41.csv
matched_cases_stp41: output/matched_cases_2020_stp41.csv
matched_all_stp41: output/matched_combined_2020_stp41.csv
match_2020_stp42:
run: python:latest python analysis/match_2020_stp42.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp42: output/matching_report_2020_stp42.txt
highly_sensitive:
matched_matches_stp42: output/matched_matches_2020_stp42.csv
matched_cases_stp42: output/matched_cases_2020_stp42.csv
matched_all_stp42: output/matched_combined_2020_stp42.csv
match_2020_stp43:
run: python:latest python analysis/match_2020_stp43.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp43: output/matching_report_2020_stp43.txt
highly_sensitive:
matched_matches_stp43: output/matched_matches_2020_stp43.csv
matched_cases_stp43: output/matched_cases_2020_stp43.csv
matched_all_stp43: output/matched_combined_2020_stp43.csv
match_2020_stp44:
run: python:latest python analysis/match_2020_stp44.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp44: output/matching_report_2020_stp44.txt
highly_sensitive:
matched_matches_stp44: output/matched_matches_2020_stp44.csv
matched_cases_stp44: output/matched_cases_2020_stp44.csv
matched_all_stp44: output/matched_combined_2020_stp44.csv
match_2020_stp49:
run: python:latest python analysis/match_2020_stp49.py
needs: [extract_asthma_matching_2020, clean_covid_matching_2020, extract_2020_matching_asthma, clean_2020_matching, split_stps_2020]
outputs:
moderately_sensitive:
matching_report_stp49: output/matching_report_2020_stp49.txt
highly_sensitive:
matched_matches_stp49: output/matched_matches_2020_stp49.csv
matched_cases_stp49: output/matched_cases_2020_stp49.csv
matched_all_stp49: output/matched_combined_2020_stp49.csv
combine_stps_covid_2020:
run: stata-mp:latest analysis/combine_stps_covid_2020.do
needs: [match_2020_stp5, match_2020_stp6, match_2020_stp7, match_2020_stp8, match_2020_stp9,
match_2020_stp10, match_2020_stp12, match_2020_stp13, match_2020_stp14, match_2020_stp15,
match_2020_stp16, match_2020_stp17, match_2020_stp20, match_2020_stp21, match_2020_stp22,
match_2020_stp23, match_2020_stp24, match_2020_stp25, match_2020_stp26, match_2020_stp27,
match_2020_stp29, match_2020_stp33, match_2020_stp35, match_2020_stp36, match_2020_stp37,
match_2020_stp40, match_2020_stp41, match_2020_stp42, match_2020_stp43, match_2020_stp44,
match_2020_stp49]
outputs:
highly_sensitive:
matched_cases_combined: output/input_combined_stps_covid_2020.csv
moderately_sensitive:
log: logs/combine_stps_covid_2020.log
combine_stps_matches_2020:
run: stata-mp:latest analysis/combine_stps_matches_2020.do
needs: [match_2020_stp5, match_2020_stp6, match_2020_stp7, match_2020_stp8, match_2020_stp9,
match_2020_stp10, match_2020_stp12, match_2020_stp13, match_2020_stp14, match_2020_stp15,
match_2020_stp16, match_2020_stp17, match_2020_stp20, match_2020_stp21, match_2020_stp22,
match_2020_stp23, match_2020_stp24, match_2020_stp25, match_2020_stp26, match_2020_stp27,
match_2020_stp29, match_2020_stp33, match_2020_stp35, match_2020_stp36, match_2020_stp37,
match_2020_stp40, match_2020_stp41, match_2020_stp42, match_2020_stp43, match_2020_stp44,
match_2020_stp49]
outputs:
highly_sensitive:
matched_matches_combined: output/input_combined_stps_matches_2020.csv
moderately_sensitive:
log: logs/combine_stps_matches_2020.log
extract_covid_2020_additional:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2020_additional
needs: [combine_stps_covid_2020]
outputs: