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Job request: 14698

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
long_term_kidney_outcomes_after_covid
ID:
65vxxbxn4beyoion
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Viyaasan Mahalingasivam requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
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

  codebook_2017_additional:
    run: stata-mp:latest analysis/codebook_2017_additional.do
    needs: [extract_covid_2017_additional, extract_2017_additional]
    outputs:
      moderately_sensitive:
        log: logs/codebook_2017_additional.log

  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

  cox_2017_case:
    run: stata-mp:latest analysis/cox_2017_case.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/cox_2017_case.log
        output: output/cox_2017_case.txt

  cox_2017_covid_severity:
    run: stata-mp:latest analysis/cox_2017_covid_severity.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/cox_2017_covid_severity.log
        output: output/cox_2017_covid_severity.txt

  cox_2017_covid_aki:
    run: stata-mp:latest analysis/cox_2017_covid_aki.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/cox_2017_covid_aki.log
        output: output/cox_2017_covid_aki.txt

  cox_2017_covid_vax:
    run: stata-mp:latest analysis/cox_2017_covid_vax.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/cox_2017_covid_vax.log
        output: output/cox_2017_covid_vax.txt

  cox_2017_wave:
    run: stata-mp:latest analysis/cox_2017_wave.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/cox_2017_wave.log
        output: output/cox_2017_wave.txt

  cox_hospitalised_case:
    run: stata-mp:latest analysis/cox_hospitalised_case.do
    needs: [analysis_hospitalised]
    outputs:
      moderately_sensitive:
        log: logs/cox_hospitalised_case.log
        output: output/cox_hospitalised_case.txt

  cox_hospitalised_covid_vax:
    run: stata-mp:latest analysis/cox_hospitalised_covid_vax.do
    needs: [analysis_hospitalised]
    outputs:
      moderately_sensitive:
        log: logs/cox_hospitalised_covid_vax.log
        output: output/cox_hospitalised_covid_vax.txt

  cox_hospitalised_wave:
    run: stata-mp:latest analysis/cox_hospitalised_wave.do
    needs: [analysis_hospitalised]
    outputs:
      moderately_sensitive:
        log: logs/cox_hospitalised_wave.log
        output: output/cox_hospitalised_wave.txt

  cox_hospitalised_case_interactions:
    run: stata-mp:latest analysis/cox_hospitalised_case_interactions.do
    needs: [analysis_hospitalised]
    outputs:
      moderately_sensitive:
        log: logs/cox_hospitalised_case_interactions.log
        output: output/cox_hospitalised_case_interactions.txt

  descriptive_2017_case:
    run: stata-mp:latest analysis/descriptive_2017_case.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/descriptive_2017_case.log
        output: output/descriptive_2017_case.csv

  descriptive_2017_covid_severity:
    run: stata-mp:latest analysis/descriptive_2017_covid_severity.do
    needs: [analysis_2017]
    outputs:
      moderately_sensitive:
        log: logs/descriptive_2017_covid_severity.log
        output: output/descriptive_2017_covid_severity.csv

  descriptive_hospitalised_case:
    run: stata-mp:latest analysis/descriptive_hospitalised_case.do
    needs: [analysis_hospitalised]
    outputs:
      moderately_sensitive:
        log: logs/descriptive_hospitalised_case.log
        output: output/descriptive_hospitalised_case.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:45:48

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
long_term_kidney_outcomes_after_covid
Requested by
Viyaasan Mahalingasivam
Branch
main
Force run dependencies
No
Git commit hash
e55cd88
Requested actions
  • descriptive_2017_case
  • descriptive_2017_covid_severity
  • descriptive_hospitalised_case