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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 30000
actions:
### study cohort ###
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_study_population_ae:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ae --index-date-range "2019-01-01 to 2023-03-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ae_*.csv.gz
generate_measures_ae:
run: cohortextractor:latest generate_measures --study-definition study_definition_ae --skip-existing --output-dir=output/measures
needs: [generate_study_population_ae]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
ae_rate_table:
run: r:latest analysis/figure/ae_rate.R
needs: [generate_measures_ae]
outputs:
moderately_sensitive:
table1: output/ae_rate_table.csv
table2: output/ae_rate_forplot.csv
plot1: output/figure_ae_rate.jpeg
infection_table:
run: r:latest analysis/figure/infection_table.R
needs: [generate_measures_ae]
outputs:
moderately_sensitive:
table1: output/infection_table.csv
table2: output/infection_forplot.csv
plot1: output/figure_infection.jpeg
generate_study_population_2ae:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2ae --index-date-range "2019-01-01 to 2023-03-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_2ae_*.csv.gz
generate_measures_2ae:
run: cohortextractor:latest generate_measures --study-definition study_definition_2ae --skip-existing --output-dir=output/measures
needs: [generate_study_population_2ae]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_2ae_*.csv
ae_rate_42days_table:
run: r:latest analysis/figure/ae_rate_42days.R
needs: [generate_measures_2ae]
outputs:
moderately_sensitive:
table1: output/ae_rate_42days_table.csv
table2: output/ae_rate_42days_forplot.csv
plot1: output/figure_ae_42days_rate.jpeg
ae_rate_42days_nocovid_table:
run: r:latest analysis/figure/ae_rate_42days_nocovid.R
needs: [generate_measures_2ae]
outputs:
moderately_sensitive:
table1: output/ae_rate_42days_nocovid_table.csv
table2: output/ae_rate_42days_nocovid_forplot.csv
plot1: output/figure_ae_42days_nocovid_rate.jpeg
###########################################################################
########## case control #########
###########################################################################
### study cohort ###
generate_study_population_case:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case
outputs:
highly_sensitive:
cohort: output/input_case.csv
### 2019-1 ###
generate_study_population_control_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1
outputs:
highly_sensitive:
cohort: output/input_control_1.csv
### 2019-2 ###
generate_study_population_control_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2
outputs:
highly_sensitive:
cohort: output/input_control_2.csv
### 2020-1 ###
generate_study_population_control_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3
outputs:
highly_sensitive:
cohort: output/input_control_3.csv
### 2020-2 ###
generate_study_population_control_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4
outputs:
highly_sensitive:
cohort: output/input_control_4.csv
### 2021-1 ###
generate_study_population_control_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5
outputs:
highly_sensitive:
cohort: output/input_control_5.csv
### 2021-2 ###
generate_study_population_control_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6
outputs:
highly_sensitive:
cohort: output/input_control_6.csv
### 2022-1 ###
generate_study_population_control_7:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7
outputs:
highly_sensitive:
cohort: output/input_control_7.csv
### 2022-2 ###
generate_study_population_control_8:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8
outputs:
highly_sensitive:
cohort: output/input_control_8.csv
### 2023-1 ###
generate_study_population_control_9:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_9
outputs:
highly_sensitive:
cohort: output/input_control_9.csv
process_1:
run: r:latest analysis/casecontrol/process_1.R
needs: [generate_study_population_case,generate_study_population_control_1,generate_study_population_control_2,
generate_study_population_control_3,generate_study_population_control_4,generate_study_population_control_5,
generate_study_population_control_6,generate_study_population_control_7,generate_study_population_control_8,
generate_study_population_control_9]
outputs:
highly_sensitive:
table1: output/case_1_uti.csv
table2: output/case_1_lrti.csv
table3: output/case_1_urti.csv
table4: output/case_1_sinusitis.csv
table5: output/case_1_ot_externa.csv
table6: output/case_1_ot_media.csv
table7: output/case_1_pneumonia.csv
table8: output/case_2_uti.csv
table9: output/case_2_lrti.csv
table10: output/case_2_urti.csv
table11: output/case_2_sinusitis.csv
table12: output/case_2_ot_externa.csv
table13: output/case_2_ot_media.csv
table14: output/case_2_pneumonia.csv
table15: output/case_3_uti.csv
table16: output/case_3_lrti.csv
table17: output/case_3_urti.csv
table18: output/case_3_sinusitis.csv
table19: output/case_3_ot_externa.csv
table20: output/case_3_ot_media.csv
table21: output/case_3_pneumonia.csv
table22: output/case_4_uti.csv
table23: output/case_4_lrti.csv
table24: output/case_4_urti.csv
table25: output/case_4_sinusitis.csv
table26: output/case_4_ot_externa.csv
table27: output/case_4_ot_media.csv
table28: output/case_4_pneumonia.csv
table29: output/case_5_uti.csv
table30: output/case_5_lrti.csv
table31: output/case_5_urti.csv
table32: output/case_5_sinusitis.csv
table33: output/case_5_ot_externa.csv
table34: output/case_5_ot_media.csv
table35: output/case_5_pneumonia.csv
table36: output/case_6_uti.csv
table37: output/case_6_lrti.csv
table38: output/case_6_urti.csv
table39: output/case_6_sinusitis.csv
table40: output/case_6_ot_externa.csv
table41: output/case_6_ot_media.csv
table42: output/case_6_pneumonia.csv
table43: output/case_7_uti.csv
table44: output/case_7_lrti.csv
table45: output/case_7_urti.csv
table46: output/case_7_sinusitis.csv
table47: output/case_7_ot_externa.csv
table48: output/case_7_ot_media.csv
table49: output/case_7_pneumonia.csv
table50: output/case_8_uti.csv
table51: output/case_8_lrti.csv
table52: output/case_8_urti.csv
table53: output/case_8_sinusitis.csv
table54: output/case_8_ot_externa.csv
table55: output/case_8_ot_media.csv
table56: output/case_8_pneumonia.csv
table57: output/case_9_uti.csv
table58: output/case_9_lrti.csv
table59: output/case_9_urti.csv
table60: output/case_9_sinusitis.csv
table61: output/case_9_ot_externa.csv
table62: output/case_9_ot_media.csv
table63: output/case_9_pneumonia.csv
table64: output/control_1_uti.csv
table65: output/control_1_lrti.csv
table66: output/control_1_urti.csv
table67: output/control_1_sinusitis.csv
table68: output/control_1_ot_externa.csv
table69: output/control_1_ot_media.csv
table70: output/control_1_pneumonia.csv
table71: output/control_2_uti.csv
table72: output/control_2_lrti.csv
table73: output/control_2_urti.csv
table74: output/control_2_sinusitis.csv
table75: output/control_2_ot_externa.csv
table76: output/control_2_ot_media.csv
table77: output/control_2_pneumonia.csv
table78: output/control_3_uti.csv
table79: output/control_3_lrti.csv
table80: output/control_3_urti.csv
table81: output/control_3_sinusitis.csv
table82: output/control_3_ot_externa.csv
table83: output/control_3_ot_media.csv
table84: output/control_3_pneumonia.csv
table85: output/control_4_uti.csv
table86: output/control_4_lrti.csv
table87: output/control_4_urti.csv
table88: output/control_4_sinusitis.csv
table89: output/control_4_ot_externa.csv
table90: output/control_4_ot_media.csv
table91: output/control_4_pneumonia.csv
table92: output/control_5_uti.csv
table93: output/control_5_lrti.csv
table94: output/control_5_urti.csv
table95: output/control_5_sinusitis.csv
table96: output/control_5_ot_externa.csv
table97: output/control_5_ot_media.csv
table98: output/control_5_pneumonia.csv
table99: output/control_6_uti.csv
table100: output/control_6_lrti.csv
table101: output/control_6_urti.csv
table102: output/control_6_sinusitis.csv
table103: output/control_6_ot_externa.csv
table104: output/control_6_ot_media.csv
table105: output/control_6_pneumonia.csv
table106: output/control_7_uti.csv
table107: output/control_7_lrti.csv
table108: output/control_7_urti.csv
table109: output/control_7_sinusitis.csv
table110: output/control_7_ot_externa.csv
table111: output/control_7_ot_media.csv
table112: output/control_7_pneumonia.csv
table113: output/control_8_uti.csv
table114: output/control_8_lrti.csv
table115: output/control_8_urti.csv
table116: output/control_8_sinusitis.csv
table117: output/control_8_ot_externa.csv
table118: output/control_8_ot_media.csv
table119: output/control_8_pneumonia.csv
table120: output/control_9_uti.csv
table121: output/control_9_lrti.csv
table122: output/control_9_urti.csv
table123: output/control_9_sinusitis.csv
table124: output/control_9_ot_externa.csv
table125: output/control_9_ot_media.csv
table126: output/control_9_pneumonia.csv
matching_1:
run: python:latest python analysis/matching_1.py
needs: [process_1]
outputs:
highly_sensitive:
table1: output/matched_cases_1_uti.csv
table2: output/matched_matches_1_uti.csv
table3: output/matched_combined_1_uti.csv
table4: output/matched_cases_1_lrti.csv
table5: output/matched_matches_1_lrti.csv
table6: output/matched_combined_1_lrti.csv
table7: output/matched_cases_1_urti.csv
table8: output/matched_matches_1_urti.csv
table9: output/matched_combined_1_urti.csv
table10: output/matched_cases_1_sinusitis.csv
table11: output/matched_matches_1_sinusitis.csv
table12: output/matched_combined_1_sinusitis.csv
table13: output/matched_cases_1_ot_externa.csv
table14: output/matched_matches_1_ot_externa.csv
table15: output/matched_combined_1_ot_externa.csv
table16: output/matched_cases_1_ot_media.csv
table17: output/matched_matches_1_ot_media.csv
table18: output/matched_combined_1_ot_media.csv
table19: output/matched_cases_1_pneumonia.csv
table20: output/matched_matches_1_pneumonia.csv
table21: output/matched_combined_1_pneumonia.csv
moderately_sensitive:
report1: output/matching_report_1_uti.txt
report2: output/matching_report_1_lrti.txt
report3: output/matching_report_1_urti.txt
report4: output/matching_report_1_sinusitis.txt
report5: output/matching_report_1_ot_externa.txt
report6: output/matching_report_1_ot_media.txt
report7: output/matching_report_1_pneumonia.txt
matching_2:
run: python:latest python analysis/matching_2.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_2_uti.csv
table23: output/matched_matches_2_uti.csv
table24: output/matched_combined_2_uti.csv
table25: output/matched_cases_2_lrti.csv
table26: output/matched_matches_2_lrti.csv
table27: output/matched_combined_2_lrti.csv
table28: output/matched_cases_2_urti.csv
table29: output/matched_matches_2_urti.csv
table30: output/matched_combined_2_urti.csv
table31: output/matched_cases_2_sinusitis.csv
table32: output/matched_matches_2_sinusitis.csv
table33: output/matched_combined_2_sinusitis.csv
table34: output/matched_cases_2_ot_externa.csv
table35: output/matched_matches_2_ot_externa.csv
table36: output/matched_combined_2_ot_externa.csv
table37: output/matched_cases_2_ot_media.csv
table38: output/matched_matches_2_ot_media.csv
table39: output/matched_combined_2_ot_media.csv
table40: output/matched_cases_2_pneumonia.csv
table41: output/matched_matches_2_pneumonia.csv
table42: output/matched_combined_2_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_2_uti.txt
report9: output/matching_report_2_lrti.txt
report10: output/matching_report_2_urti.txt
report11: output/matching_report_2_sinusitis.txt
report12: output/matching_report_2_ot_externa.txt
report13: output/matching_report_2_ot_media.txt
report14: output/matching_report_2_pneumonia.txt
matching_3:
run: python:latest python analysis/matching_3.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_3_uti.csv
table23: output/matched_matches_3_uti.csv
table24: output/matched_combined_3_uti.csv
table25: output/matched_cases_3_lrti.csv
table26: output/matched_matches_3_lrti.csv
table27: output/matched_combined_3_lrti.csv
table28: output/matched_cases_3_urti.csv
table29: output/matched_matches_3_urti.csv
table30: output/matched_combined_3_urti.csv
table31: output/matched_cases_3_sinusitis.csv
table32: output/matched_matches_3_sinusitis.csv
table33: output/matched_combined_3_sinusitis.csv
table34: output/matched_cases_3_ot_externa.csv
table35: output/matched_matches_3_ot_externa.csv
table36: output/matched_combined_3_ot_externa.csv
table37: output/matched_cases_3_ot_media.csv
table38: output/matched_matches_3_ot_media.csv
table39: output/matched_combined_3_ot_media.csv
table40: output/matched_cases_3_pneumonia.csv
table41: output/matched_matches_3_pneumonia.csv
table42: output/matched_combined_3_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_3_uti.txt
report9: output/matching_report_3_lrti.txt
report10: output/matching_report_3_urti.txt
report11: output/matching_report_3_sinusitis.txt
report12: output/matching_report_3_ot_externa.txt
report13: output/matching_report_3_ot_media.txt
report14: output/matching_report_3_pneumonia.txt
matching_4:
run: python:latest python analysis/matching_4.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_4_uti.csv
table23: output/matched_matches_4_uti.csv
table24: output/matched_combined_4_uti.csv
table25: output/matched_cases_4_lrti.csv
table26: output/matched_matches_4_lrti.csv
table27: output/matched_combined_4_lrti.csv
table28: output/matched_cases_4_urti.csv
table29: output/matched_matches_4_urti.csv
table30: output/matched_combined_4_urti.csv
table31: output/matched_cases_4_sinusitis.csv
table32: output/matched_matches_4_sinusitis.csv
table33: output/matched_combined_4_sinusitis.csv
table34: output/matched_cases_4_ot_externa.csv
table35: output/matched_matches_4_ot_externa.csv
table36: output/matched_combined_4_ot_externa.csv
table37: output/matched_cases_4_ot_media.csv
table38: output/matched_matches_4_ot_media.csv
table39: output/matched_combined_4_ot_media.csv
table40: output/matched_cases_4_pneumonia.csv
table41: output/matched_matches_4_pneumonia.csv
table42: output/matched_combined_4_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_4_uti.txt
report9: output/matching_report_4_lrti.txt
report10: output/matching_report_4_urti.txt
report11: output/matching_report_4_sinusitis.txt
report12: output/matching_report_4_ot_externa.txt
report13: output/matching_report_4_ot_media.txt
report14: output/matching_report_4_pneumonia.txt
matching_5:
run: python:latest python analysis/matching_5.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_5_uti.csv
table23: output/matched_matches_5_uti.csv
table24: output/matched_combined_5_uti.csv
table25: output/matched_cases_5_lrti.csv
table26: output/matched_matches_5_lrti.csv
table27: output/matched_combined_5_lrti.csv
table28: output/matched_cases_5_urti.csv
table29: output/matched_matches_5_urti.csv
table30: output/matched_combined_5_urti.csv
table31: output/matched_cases_5_sinusitis.csv
table32: output/matched_matches_5_sinusitis.csv
table33: output/matched_combined_5_sinusitis.csv
table34: output/matched_cases_5_ot_externa.csv
table35: output/matched_matches_5_ot_externa.csv
table36: output/matched_combined_5_ot_externa.csv
table37: output/matched_cases_5_ot_media.csv
table38: output/matched_matches_5_ot_media.csv
table39: output/matched_combined_5_ot_media.csv
table40: output/matched_cases_5_pneumonia.csv
table41: output/matched_matches_5_pneumonia.csv
table42: output/matched_combined_5_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_5_uti.txt
report9: output/matching_report_5_lrti.txt
report10: output/matching_report_5_urti.txt
report11: output/matching_report_5_sinusitis.txt
report12: output/matching_report_5_ot_externa.txt
report13: output/matching_report_5_ot_media.txt
report14: output/matching_report_5_pneumonia.txt
matching_6:
run: python:latest python analysis/matching_6.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_6_uti.csv
table23: output/matched_matches_6_uti.csv
table24: output/matched_combined_6_uti.csv
table25: output/matched_cases_6_lrti.csv
table26: output/matched_matches_6_lrti.csv
table27: output/matched_combined_6_lrti.csv
table28: output/matched_cases_6_urti.csv
table29: output/matched_matches_6_urti.csv
table30: output/matched_combined_6_urti.csv
table31: output/matched_cases_6_sinusitis.csv
table32: output/matched_matches_6_sinusitis.csv
table33: output/matched_combined_6_sinusitis.csv
table34: output/matched_cases_6_ot_externa.csv
table35: output/matched_matches_6_ot_externa.csv
table36: output/matched_combined_6_ot_externa.csv
table37: output/matched_cases_6_ot_media.csv
table38: output/matched_matches_6_ot_media.csv
table39: output/matched_combined_6_ot_media.csv
table40: output/matched_cases_6_pneumonia.csv
table41: output/matched_matches_6_pneumonia.csv
table42: output/matched_combined_6_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_6_uti.txt
report9: output/matching_report_6_lrti.txt
report10: output/matching_report_6_urti.txt
report11: output/matching_report_6_sinusitis.txt
report12: output/matching_report_6_ot_externa.txt
report13: output/matching_report_6_ot_media.txt
report14: output/matching_report_6_pneumonia.txt
matching_7:
run: python:latest python analysis/matching_7.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_7_uti.csv
table23: output/matched_matches_7_uti.csv
table24: output/matched_combined_7_uti.csv
table25: output/matched_cases_7_lrti.csv
table26: output/matched_matches_7_lrti.csv
table27: output/matched_combined_7_lrti.csv
table28: output/matched_cases_7_urti.csv
table29: output/matched_matches_7_urti.csv
table30: output/matched_combined_7_urti.csv
table31: output/matched_cases_7_sinusitis.csv
table32: output/matched_matches_7_sinusitis.csv
table33: output/matched_combined_7_sinusitis.csv
table34: output/matched_cases_7_ot_externa.csv
table35: output/matched_matches_7_ot_externa.csv
table36: output/matched_combined_7_ot_externa.csv
table37: output/matched_cases_7_ot_media.csv
table38: output/matched_matches_7_ot_media.csv
table39: output/matched_combined_7_ot_media.csv
table40: output/matched_cases_7_pneumonia.csv
table41: output/matched_matches_7_pneumonia.csv
table42: output/matched_combined_7_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_7_uti.txt
report9: output/matching_report_7_lrti.txt
report10: output/matching_report_7_urti.txt
report11: output/matching_report_7_sinusitis.txt
report12: output/matching_report_7_ot_externa.txt
report13: output/matching_report_7_ot_media.txt
report14: output/matching_report_7_pneumonia.txt
matching_8:
run: python:latest python analysis/matching_8.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_8_uti.csv
table23: output/matched_matches_8_uti.csv
table24: output/matched_combined_8_uti.csv
table25: output/matched_cases_8_lrti.csv
table26: output/matched_matches_8_lrti.csv
table27: output/matched_combined_8_lrti.csv
table28: output/matched_cases_8_urti.csv
table29: output/matched_matches_8_urti.csv
table30: output/matched_combined_8_urti.csv
table31: output/matched_cases_8_sinusitis.csv
table32: output/matched_matches_8_sinusitis.csv
table33: output/matched_combined_8_sinusitis.csv
table34: output/matched_cases_8_ot_externa.csv
table35: output/matched_matches_8_ot_externa.csv
table36: output/matched_combined_8_ot_externa.csv
table37: output/matched_cases_8_ot_media.csv
table38: output/matched_matches_8_ot_media.csv
table39: output/matched_combined_8_ot_media.csv
table40: output/matched_cases_8_pneumonia.csv
table41: output/matched_matches_8_pneumonia.csv
table42: output/matched_combined_8_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_8_uti.txt
report9: output/matching_report_8_lrti.txt
report10: output/matching_report_8_urti.txt
report11: output/matching_report_8_sinusitis.txt
report12: output/matching_report_8_ot_externa.txt
report13: output/matching_report_8_ot_media.txt
report14: output/matching_report_8_pneumonia.txt
matching_9:
run: python:latest python analysis/matching_9.py
needs: [process_1]
outputs:
highly_sensitive:
table22: output/matched_cases_9_uti.csv
table23: output/matched_matches_9_uti.csv
table24: output/matched_combined_9_uti.csv
table25: output/matched_cases_9_lrti.csv
table26: output/matched_matches_9_lrti.csv
table27: output/matched_combined_9_lrti.csv
table28: output/matched_cases_9_urti.csv
table29: output/matched_matches_9_urti.csv
table30: output/matched_combined_9_urti.csv
table31: output/matched_cases_9_sinusitis.csv
table32: output/matched_matches_9_sinusitis.csv
table33: output/matched_combined_9_sinusitis.csv
table34: output/matched_cases_9_ot_externa.csv
table35: output/matched_matches_9_ot_externa.csv
table36: output/matched_combined_9_ot_externa.csv
table37: output/matched_cases_9_ot_media.csv
table38: output/matched_matches_9_ot_media.csv
table39: output/matched_combined_9_ot_media.csv
table40: output/matched_cases_9_pneumonia.csv
table41: output/matched_matches_9_pneumonia.csv
table42: output/matched_combined_9_pneumonia.csv
moderately_sensitive:
report8: output/matching_report_9_uti.txt
report9: output/matching_report_9_lrti.txt
report10: output/matching_report_9_urti.txt
report11: output/matching_report_9_sinusitis.txt
report12: output/matching_report_9_ot_externa.txt
report13: output/matching_report_9_ot_media.txt
report14: output/matching_report_9_pneumonia.txt
process_2:
run: r:latest analysis/casecontrol/process_2.R
needs: [matching_1,matching_2,matching_3,matching_4,matching_5,matching_6,matching_7,matching_8,matching_9]
outputs:
highly_sensitive:
table1: output/cases_uti.csv
table2: output/cases_lrti.csv
table3: output/cases_urti.csv
table4: output/cases_sinusitis.csv
table5: output/cases_ot_externa.csv
table6: output/cases_ot_media.csv
table7: output/cases_pneumonia.csv
moderately_sensitive:
table8: output/summary_table.csv
#### Extracting cases variables for each infection type ####
# UTI
generate_study_population_case_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_uti_var_1.csv
generate_study_population_case_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_uti_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_uti_var_2.csv
# LRTI
generate_study_population_case_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_lrti_var_1.csv
generate_study_population_case_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_lrti_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_lrti_var_2.csv
# URTI
generate_study_population_case_urti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_urti_var_1.csv
generate_study_population_case_urti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_urti_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_urti_var_2.csv
# Sinusitis
generate_study_population_case_sinusitis_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_sinusitis_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_sinusitis_var_1.csv
generate_study_population_case_sinusitis_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_sinusitis_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_sinusitis_var_2.csv
# Otitis Externa
generate_study_population_case_ot_externa_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ot_externa_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_ot_externa_var_1.csv
generate_study_population_case_ot_externa_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ot_externa_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_ot_externa_var_2.csv
# Otitis Media
generate_study_population_case_ot_media_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ot_media_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_ot_media_var_1.csv
generate_study_population_case_ot_media_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ot_media_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_ot_media_var_2.csv
# Pneumonia
generate_study_population_case_pneumonia_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_pneumonia_var_1
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_pneumonia_var_1.csv
generate_study_population_case_pneumonia_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_pneumonia_var_2
needs: [process_2]
outputs:
highly_sensitive:
cohort: output/input_case_pneumonia_var_2.csv
#### Extracting controls variables ####
# UTI
generate_study_population_control_1_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_uti_var_1
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_uti_var_1.csv
generate_study_population_control_1_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_uti_var_2
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_uti_var_2.csv
generate_study_population_control_2_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_uti_var_1
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_uti_var_1.csv
generate_study_population_control_2_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_uti_var_2
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_uti_var_2.csv
generate_study_population_control_3_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_uti_var_1
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_uti_var_1.csv
generate_study_population_control_3_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_uti_var_2
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_uti_var_2.csv
generate_study_population_control_4_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4_uti_var_1
needs: [matching_4]
outputs:
highly_sensitive:
cohort: output/input_control_4_uti_var_1.csv
generate_study_population_control_4_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4_uti_var_2
needs: [matching_4]
outputs:
highly_sensitive:
cohort: output/input_control_4_uti_var_2.csv
generate_study_population_control_5_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5_uti_var_1
needs: [matching_5]
outputs:
highly_sensitive:
cohort: output/input_control_5_uti_var_1.csv
generate_study_population_control_5_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5_uti_var_2
needs: [matching_5]
outputs:
highly_sensitive:
cohort: output/input_control_5_uti_var_2.csv
generate_study_population_control_6_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6_uti_var_1
needs: [matching_6]
outputs:
highly_sensitive:
cohort: output/input_control_6_uti_var_1.csv
generate_study_population_control_6_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6_uti_var_2
needs: [matching_6]
outputs:
highly_sensitive:
cohort: output/input_control_6_uti_var_2.csv
generate_study_population_control_7_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7_uti_var_1
needs: [matching_7]
outputs:
highly_sensitive:
cohort: output/input_control_7_uti_var_1.csv
generate_study_population_control_7_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7_uti_var_2
needs: [matching_7]
outputs:
highly_sensitive:
cohort: output/input_control_7_uti_var_2.csv
generate_study_population_control_8_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8_uti_var_1
needs: [matching_8]
outputs:
highly_sensitive:
cohort: output/input_control_8_uti_var_1.csv
generate_study_population_control_8_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8_uti_var_2
needs: [matching_8]
outputs:
highly_sensitive:
cohort: output/input_control_8_uti_var_2.csv
generate_study_population_control_9_uti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_9_uti_var_1
needs: [matching_9]
outputs:
highly_sensitive:
cohort: output/input_control_9_uti_var_1.csv
generate_study_population_control_9_uti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_9_uti_var_2
needs: [matching_9]
outputs:
highly_sensitive:
cohort: output/input_control_9_uti_var_2.csv
# LRTI
generate_study_population_control_1_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_lrti_var_1
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_lrti_var_1.csv
generate_study_population_control_1_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_lrti_var_2
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_lrti_var_2.csv
generate_study_population_control_2_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_lrti_var_1
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_lrti_var_1.csv
generate_study_population_control_2_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_lrti_var_2
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_lrti_var_2.csv
generate_study_population_control_3_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_lrti_var_1
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_lrti_var_1.csv
generate_study_population_control_3_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_lrti_var_2
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_lrti_var_2.csv
generate_study_population_control_4_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4_lrti_var_1
needs: [matching_4]
outputs:
highly_sensitive:
cohort: output/input_control_4_lrti_var_1.csv
generate_study_population_control_4_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4_lrti_var_2
needs: [matching_4]
outputs:
highly_sensitive:
cohort: output/input_control_4_lrti_var_2.csv
generate_study_population_control_5_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5_lrti_var_1
needs: [matching_5]
outputs:
highly_sensitive:
cohort: output/input_control_5_lrti_var_1.csv
generate_study_population_control_5_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5_lrti_var_2
needs: [matching_5]
outputs:
highly_sensitive:
cohort: output/input_control_5_lrti_var_2.csv
generate_study_population_control_6_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6_lrti_var_1
needs: [matching_6]
outputs:
highly_sensitive:
cohort: output/input_control_6_lrti_var_1.csv
generate_study_population_control_6_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6_lrti_var_2
needs: [matching_6]
outputs:
highly_sensitive:
cohort: output/input_control_6_lrti_var_2.csv
generate_study_population_control_7_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7_lrti_var_1
needs: [matching_7]
outputs:
highly_sensitive:
cohort: output/input_control_7_lrti_var_1.csv
generate_study_population_control_7_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7_lrti_var_2
needs: [matching_7]
outputs:
highly_sensitive:
cohort: output/input_control_7_lrti_var_2.csv
generate_study_population_control_8_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8_lrti_var_1
needs: [matching_8]
outputs:
highly_sensitive:
cohort: output/input_control_8_lrti_var_1.csv
generate_study_population_control_8_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8_lrti_var_2
needs: [matching_8]
outputs:
highly_sensitive:
cohort: output/input_control_8_lrti_var_2.csv
generate_study_population_control_9_lrti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_9_lrti_var_1
needs: [matching_9]
outputs:
highly_sensitive:
cohort: output/input_control_9_lrti_var_1.csv
generate_study_population_control_9_lrti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_9_lrti_var_2
needs: [matching_9]
outputs:
highly_sensitive:
cohort: output/input_control_9_lrti_var_2.csv
# URTI
generate_study_population_control_1_urti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_urti_var_1
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_urti_var_1.csv
generate_study_population_control_1_urti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1_urti_var_2
needs: [matching_1]
outputs:
highly_sensitive:
cohort: output/input_control_1_urti_var_2.csv
generate_study_population_control_2_urti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_urti_var_1
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_urti_var_1.csv
generate_study_population_control_2_urti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2_urti_var_2
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_control_2_urti_var_2.csv
generate_study_population_control_3_urti_var_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_urti_var_1
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_urti_var_1.csv
generate_study_population_control_3_urti_var_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3_urti_var_2
needs: [matching_3]
outputs:
highly_sensitive:
cohort: output/input_control_3_urti_var_2.csv