Job request: 7524

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Nick Kennedy requested one or more actions to be run against real patient data in the Immunosuppresant Medication 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

ID Status Action
suwb7ufarpoghqty failed run_forest_plots
zql7xe2lzfbpkksk failed run_forest_plots_ethnicity
kpg7cmmun7zspkfw failed run_forest_plots_ethnicity_vs_white

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 50000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  create_cohorts:
    run: stata-mp:latest analysis/000_define_covariates.do
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        log1: logs/start_create_analysis_dataset.smcl 
        data1: output/data/file_imid.dta
        data2: output/data/file_joint.dta
        data3: output/data/file_skin.dta
        data4: output/data/file_bowel.dta
        data5: output/data/file_imiddrugcategory.dta
        data6: output/data/file_standtnf.dta
        data7: output/data/file_standtnf3m.dta
        data8: output/data/file_tnfmono.dta
        data9: output/data/file_standil6.dta
        data10: output/data/file_standil17.dta
        data11: output/data/file_standil23.dta
        data12: output/data/file_standjaki.dta
        data13: output/data/file_standritux.dta
        data14: output/data/file_standinflix.dta
        data15: output/data/file_standvedolizumab.dta
        data16: output/data/file_standabatacept.dta

  create_cohorts_single_file:
    run: stata-mp:latest analysis/001_define_covariates_single_file.do
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        log1: logs/start_create_analysis_dataset_single_file.smcl 
        data1: output/data/file_imid_all.dta

  run_baseline_tables:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/descriptive_tables.smcl 
      
  run_cox_models_imid:
    run: stata-mp:latest analysis/202_cox_models.do "imid"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid.smcl 
        data1: output/data/cox_model_summary_imid.dta
        data2: output/data/cox_model_summary_haemonc_imid.dta
        
  run_cox_models_joint:
    run: stata-mp:latest analysis/202_cox_models.do "joint"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint.smcl 
        data1: output/data/cox_model_summary_joint.dta
        data2: output/data/cox_model_summary_haemonc_joint.dta

  run_cox_models_skin:
    run: stata-mp:latest analysis/202_cox_models.do "skin"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin.smcl 
        data1: output/data/cox_model_summary_skin.dta
        data2: output/data/cox_model_summary_haemonc_skin.dta
 
  run_cox_models_bowel:
    run: stata-mp:latest analysis/202_cox_models.do "bowel"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel.smcl 
        data1: output/data/cox_model_summary_bowel.dta
        data2: output/data/cox_model_summary_haemonc_bowel.dta
 
  run_cox_models_imiddrugcategory:
    run: stata-mp:latest analysis/202_cox_models.do "imiddrugcategory"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imiddrugcategory.smcl 
        data1: output/data/cox_model_summary_imiddrugcategory.dta
        data2: output/data/cox_model_summary_haemonc_imiddrugcategory.dta
  
  run_cox_models_standtnf:
    run: stata-mp:latest analysis/202_cox_models.do "standtnf"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standtnf.smcl 
        data1: output/data/cox_model_summary_standtnf.dta
        data2: output/data/cox_model_summary_haemonc_standtnf.dta

  run_cox_models_standtnf3m:
    run: stata-mp:latest analysis/202_cox_models.do "standtnf3m"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standtnf3m.smcl 
        data1: output/data/cox_model_summary_standtnf3m.dta
        data2: output/data/cox_model_summary_haemonc_standtnf3m.dta
       
  run_cox_models_tnfmono:
    run: stata-mp:latest analysis/202_cox_models.do "tnfmono"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_tnfmono.smcl 
        data1: output/data/cox_model_summary_tnfmono.dta
        data2: output/data/cox_model_summary_haemonc_tnfmono.dta
  
  run_cox_models_standil6:
    run: stata-mp:latest analysis/202_cox_models.do "standil6"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil6.smcl 
        data1: output/data/cox_model_summary_standil6.dta
        data2: output/data/cox_model_summary_haemonc_standil6.dta
  
  run_cox_models_standil17:
    run: stata-mp:latest analysis/202_cox_models.do "standil17"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil17.smcl 
        data1: output/data/cox_model_summary_standil17.dta
        data2: output/data/cox_model_summary_haemonc_standil17.dta
 
  run_cox_models_standil23:
    run: stata-mp:latest analysis/202_cox_models.do "standil23"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil23.smcl 
        data1: output/data/cox_model_summary_standil23.dta
        data2: output/data/cox_model_summary_haemonc_standil23.dta
 
  run_cox_models_standjaki:
    run: stata-mp:latest analysis/202_cox_models.do "standjaki"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standjaki.smcl 
        data1: output/data/cox_model_summary_standjaki.dta
        data2: output/data/cox_model_summary_haemonc_standjaki.dta
  
  run_cox_models_standritux:
    run: stata-mp:latest analysis/202_cox_models.do "standritux"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standritux.smcl 
        data1: output/data/cox_model_summary_standritux.dta
        data2: output/data/cox_model_summary_haemonc_standritux.dta
        
  run_cox_models_standinflix:
    run: stata-mp:latest analysis/202_cox_models.do "standinflix"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standinflix.smcl 
        data1: output/data/cox_model_summary_standinflix.dta
        data2: output/data/cox_model_summary_haemonc_standinflix.dta

  run_cox_models_standvedolizumab:
    run: stata-mp:latest analysis/202_cox_models.do "standvedolizumab"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standvedolizumab.smcl 
        data1: output/data/cox_model_summary_standvedolizumab.dta
        data2: output/data/cox_model_summary_haemonc_standvedolizumab.dta

  run_cox_models_standabatacept:
    run: stata-mp:latest analysis/202_cox_models.do "standabatacept"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standabatacept.smcl 
        data1: output/data/cox_model_summary_standabatacept.dta
        data2: output/data/cox_model_summary_haemonc_standabatacept.dta
        
  run_cox_models_imid_ethnicity_1:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "1"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_1.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_1.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_1.dta

  run_cox_models_imid_ethnicity_2:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "2"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_2.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_2.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_2.dta

  run_cox_models_imid_ethnicity_3:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "3"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_3.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_3.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_3.dta

  run_cox_models_imid_ethnicity_4:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "4"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_4.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_4.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_4.dta

  run_cox_models_imid_ethnicity_5:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "5"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_5.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_5.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_5.dta

  run_cox_models_imid_ethnicity_u:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "u"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_u.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_u.dta
        data2: output/data/cox_model_summary_haemonc_imid_ethnicity_u.dta

  run_cox_models_joint_ethnicity_1:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "1"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_1.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_1.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_1.dta

  run_cox_models_joint_ethnicity_2:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "2"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_2.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_2.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_2.dta

  run_cox_models_joint_ethnicity_3:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "3"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_3.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_3.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_3.dta

  run_cox_models_joint_ethnicity_4:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "4"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_4.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_4.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_4.dta

  run_cox_models_joint_ethnicity_5:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "5"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_5.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_5.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_5.dta

  run_cox_models_joint_ethnicity_u:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "u"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_u.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_u.dta
        data2: output/data/cox_model_summary_haemonc_joint_ethnicity_u.dta

  run_cox_models_skin_ethnicity_1:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "1"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_1.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_1.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_1.dta

  run_cox_models_skin_ethnicity_2:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "2"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_2.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_2.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_2.dta

  run_cox_models_skin_ethnicity_3:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "3"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_3.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_3.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_3.dta

  run_cox_models_skin_ethnicity_4:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "4"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_4.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_4.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_4.dta

  run_cox_models_skin_ethnicity_5:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "5"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_5.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_5.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_5.dta

  run_cox_models_skin_ethnicity_u:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "u"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_u.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_u.dta
        data2: output/data/cox_model_summary_haemonc_skin_ethnicity_u.dta

  run_cox_models_bowel_ethnicity_1:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "1"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_1.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_1.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_1.dta

  run_cox_models_bowel_ethnicity_2:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "2"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_2.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_2.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_2.dta

  run_cox_models_bowel_ethnicity_3:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "3"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_3.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_3.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_3.dta

  run_cox_models_bowel_ethnicity_4:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "4"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_4.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_4.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_4.dta

  run_cox_models_bowel_ethnicity_5:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "5"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_5.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_5.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_5.dta

  run_cox_models_bowel_ethnicity_u:
    run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "u"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_u.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_u.dta
        data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_u.dta

  run_cox_models_genpop_ethnicity_vs_white:
    run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "genpop"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_genpop_ethnicity_vs_white.smcl 
        data1: output/data/cox_model_summary_genpop_ethnicity_vs_white.dta

  run_cox_models_imid_ethnicity_vs_white:
    run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "imid"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid_ethnicity_vs_white.smcl 
        data1: output/data/cox_model_summary_imid_ethnicity_vs_white.dta

  run_cox_models_joint_ethnicity_vs_white:
    run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "joint"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint_ethnicity_vs_white.smcl 
        data1: output/data/cox_model_summary_joint_ethnicity_vs_white.dta

  run_cox_models_skin_ethnicity_vs_white:
    run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "skin"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin_ethnicity_vs_white.smcl 
        data1: output/data/cox_model_summary_skin_ethnicity_vs_white.dta

  run_cox_models_bowel_ethnicity_vs_white:
    run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "bowel"
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel_ethnicity_vs_white.smcl 
        data1: output/data/cox_model_summary_bowel_ethnicity_vs_white.dta

  run_survival_curves:
    run: stata-mp:latest analysis/301_survival_curves.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/graphs.smcl 
        survcur_bowel_died: output/figures/survcur_bowel_died.svg
        survcur_bowel_hospital: output/figures/survcur_bowel_hospital.svg
        survcur_bowel_icuordeath: output/figures/survcur_bowel_icuordeath.svg
        survcur_imid_died: output/figures/survcur_imid_died.svg
        survcur_imid_hospital: output/figures/survcur_imid_hospital.svg
        survcur_imid_icuordeath: output/figures/survcur_imid_icuordeath.svg
        survcur_imiddrugcategory_died: output/figures/survcur_imiddrugcategory_died.svg
        survcur_imiddrugcategory_hospital: output/figures/survcur_imiddrugcategory_hospital.svg
        survcur_imiddrugcategory_icuordeath: output/figures/survcur_imiddrugcategory_icuordeath.svg
        survcur_joint_died: output/figures/survcur_joint_died.svg
        survcur_joint_hospital: output/figures/survcur_joint_hospital.svg
        survcur_joint_icuordeath: output/figures/survcur_joint_icuordeath.svg
        survcur_skin_died: output/figures/survcur_skin_died.svg
        survcur_skin_hospital: output/figures/survcur_skin_hospital.svg
        survcur_skin_icuordeath: output/figures/survcur_skin_icuordeath.svg
        survhaz_bowel_died: output/figures/survhaz_bowel_died.svg
        survhaz_bowel_hospital: output/figures/survhaz_bowel_hospital.svg
        survhaz_bowel_icuordeath: output/figures/survhaz_bowel_icuordeath.svg
        survhaz_imid_died: output/figures/survhaz_imid_died.svg
        survhaz_imid_hospital: output/figures/survhaz_imid_hospital.svg
        survhaz_imid_icuordeath: output/figures/survhaz_imid_icuordeath.svg
        survhaz_imiddrugcategory_died: output/figures/survhaz_imiddrugcategory_died.svg
        survhaz_imiddrugcategory_hospital: output/figures/survhaz_imiddrugcategory_hospital.svg
        survhaz_imiddrugcategory_icuordeath: output/figures/survhaz_imiddrugcategory_icuordeath.svg
        survhaz_joint_died: output/figures/survhaz_joint_died.svg
        survhaz_joint_hospital: output/figures/survhaz_joint_hospital.svg
        survhaz_joint_icuordeath: output/figures/survhaz_joint_icuordeath.svg
        survhaz_skin_died: output/figures/survhaz_skin_died.svg
        survhaz_skin_hospital: output/figures/survhaz_skin_hospital.svg
        survhaz_skin_icuordeath: output/figures/survhaz_skin_icuordeath.svg
        survrisk_bowel_died: output/figures/survrisk_bowel_died.svg
        survrisk_bowel_hospital: output/figures/survrisk_bowel_hospital.svg
        survrisk_bowel_icuordeath: output/figures/survrisk_bowel_icuordeath.svg
        survrisk_imid_died: output/figures/survrisk_imid_died.svg
        survrisk_imid_hospital: output/figures/survrisk_imid_hospital.svg
        survrisk_imid_icuordeath: output/figures/survrisk_imid_icuordeath.svg
        survrisk_imiddrugcategory_died: output/figures/survrisk_imiddrugcategory_died.svg
        survrisk_imiddrugcategory_hospital: output/figures/survrisk_imiddrugcategory_hospital.svg
        survrisk_imiddrugcategory_icuordeath: output/figures/survrisk_imiddrugcategory_icuordeath.svg
        survrisk_joint_died: output/figures/survrisk_joint_died.svg
        survrisk_joint_hospital: output/figures/survrisk_joint_hospital.svg
        survrisk_joint_icuordeath: output/figures/survrisk_joint_icuordeath.svg
        survrisk_skin_died: output/figures/survrisk_skin_died.svg
        survrisk_skin_hospital: output/figures/survrisk_skin_hospital.svg
        survrisk_skin_icuordeath: output/figures/survrisk_skin_icuordeath.svg

  run_cox_spline_imid:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "imid"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_imid.smcl 
        data1: output/data/cox_spline_summary_imid.dta
        data2: output/data/cox_spline_summary_haemonc_imid.dta
        
  run_cox_spline_joint:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "joint"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_joint.smcl 
        data1: output/data/cox_spline_summary_joint.dta
        data2: output/data/cox_spline_summary_haemonc_joint.dta

  run_cox_spline_skin:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "skin"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_skin.smcl 
        data1: output/data/cox_spline_summary_skin.dta
        data2: output/data/cox_spline_summary_haemonc_skin.dta
 
  run_cox_spline_bowel:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "bowel"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_bowel.smcl 
        data1: output/data/cox_spline_summary_bowel.dta
        data2: output/data/cox_spline_summary_haemonc_bowel.dta
 
  run_cox_spline_imiddrugcategory:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "imiddrugcategory"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_imiddrugcategory.smcl 
        data1: output/data/cox_spline_summary_imiddrugcategory.dta
        data2: output/data/cox_spline_summary_haemonc_imiddrugcategory.dta
  
  run_cox_spline_standtnf:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standtnf"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standtnf.smcl 
        data1: output/data/cox_spline_summary_standtnf.dta
        data2: output/data/cox_spline_summary_haemonc_standtnf.dta

  run_cox_spline_standtnf3m:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standtnf3m"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standtnf3m.smcl 
        data1: output/data/cox_spline_summary_standtnf3m.dta
        data2: output/data/cox_spline_summary_haemonc_standtnf3m.dta
       
  run_cox_spline_tnfmono:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "tnfmono"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_tnfmono.smcl 
        data1: output/data/cox_spline_summary_tnfmono.dta
        data2: output/data/cox_spline_summary_haemonc_tnfmono.dta
  
  run_cox_spline_standil6:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standil6"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standil6.smcl 
        data1: output/data/cox_spline_summary_standil6.dta
        data2: output/data/cox_spline_summary_haemonc_standil6.dta
  
  run_cox_spline_standil17:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standil17"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standil17.smcl 
        data1: output/data/cox_spline_summary_standil17.dta
        data2: output/data/cox_spline_summary_haemonc_standil17.dta
 
  run_cox_spline_standil23:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standil23"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standil23.smcl 
        data1: output/data/cox_spline_summary_standil23.dta
        data2: output/data/cox_spline_summary_haemonc_standil23.dta
 
  run_cox_spline_standjaki:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standjaki"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standjaki.smcl 
        data1: output/data/cox_spline_summary_standjaki.dta
        data2: output/data/cox_spline_summary_haemonc_standjaki.dta
  
  run_cox_spline_standritux:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standritux"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standritux.smcl 
        data1: output/data/cox_spline_summary_standritux.dta
        data2: output/data/cox_spline_summary_haemonc_standritux.dta
        
  run_cox_spline_standinflix:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standinflix"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standinflix.smcl 
        data1: output/data/cox_spline_summary_standinflix.dta
        data2: output/data/cox_spline_summary_haemonc_standinflix.dta

  run_cox_spline_standvedolizumab:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standvedolizumab"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standvedolizumab.smcl 
        data1: output/data/cox_spline_summary_standvedolizumab.dta
        data2: output/data/cox_spline_summary_haemonc_standvedolizumab.dta

  run_cox_spline_standabatacept:
    run: stata-mp:latest analysis/402_cox_models_agespline.do "standabatacept"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_spline_standabatacept.smcl 
        data1: output/data/cox_spline_summary_standabatacept.dta
        data2: output/data/cox_spline_summary_haemonc_standabatacept.dta

  run_spline_export_csv:
    run: stata-mp:latest analysis/403_spline_export_csv.do
    needs: [run_cox_spline_imid,run_cox_spline_joint,run_cox_spline_bowel,run_cox_spline_skin,run_cox_spline_imiddrugcategory,run_cox_spline_standtnf,run_cox_spline_standtnf3m,run_cox_spline_standil6,run_cox_spline_standil17,run_cox_spline_standil23,run_cox_spline_standritux,run_cox_spline_standinflix,run_cox_spline_tnfmono,run_cox_spline_standjaki,run_cox_spline_standvedolizumab,run_cox_spline_standabatacept]
    outputs:
      moderately_sensitive:
        log: logs/spline_export_csv.smcl
        csv_spline_spline_imid: output/data/csv_spline_imid.csv
        csvhaemonc_spline_imid: output/data/csvhaemonc_spline_imid.csv
        csv_spline_joint: output/data/csv_spline_joint.csv
        csvhaemonc_spline_joint: output/data/csvhaemonc_spline_joint.csv
        csv_spline_skin: output/data/csv_spline_skin.csv
        csvhaemonc_spline_skin: output/data/csvhaemonc_spline_skin.csv
        csv_spline_bowel: output/data/csv_spline_bowel.csv
        csvhaemonc_spline_bowel: output/data/csvhaemonc_spline_bowel.csv
        csv_spline_imiddrugcategory: output/data/csv_spline_imiddrugcategory.csv
        csvhaemonc_spline_imiddrugcategory: output/data/csvhaemonc_spline_imiddrugcategory.csv
        csv_spline_standtnf: output/data/csv_spline_standtnf.csv
        csvhaemonc_spline_standtnf: output/data/csvhaemonc_spline_standtnf.csv
        csv_spline_standtnf3m: output/data/csv_spline_standtnf3m.csv
        csvhaemonc_spline_standtnf3m: output/data/csvhaemonc_spline_standtnf3m.csv
        csv_spline_tnfmono: output/data/csv_spline_tnfmono.csv
        csvhaemonc_spline_tnfmono: output/data/csvhaemonc_spline_tnfmono.csv
        csv_spline_standil6: output/data/csv_spline_standil6.csv
        csvhaemonc_spline_standil6: output/data/csvhaemonc_spline_standil6.csv
        csv_spline_standil17: output/data/csv_spline_standil17.csv
        csvhaemonc_spline_standil17: output/data/csvhaemonc_spline_standil17.csv
        csv_spline_standil23: output/data/csv_spline_standil23.csv
        csvhaemonc_spline_standil23: output/data/csvhaemonc_spline_standil23.csv
        csv_spline_standjaki: output/data/csv_spline_standjaki.csv
        csvhaemonc_spline_standjaki: output/data/csvhaemonc_spline_standjaki.csv
        csv_spline_standritux: output/data/csv_spline_standritux.csv
        csvhaemonc_spline_standritux: output/data/csvhaemonc_spline_standritux.csv
        csv_spline_standinflix: output/data/csv_spline_standinflix.csv
        csvhaemonc_spline_standinflix: output/data/csvhaemonc_spline_standinflix.csv
        csv_spline_standvedolizumab: output/data/csv_spline_standvedolizumab.csv
        csvhaemonc_spline_standvedolizumab: output/data/csvhaemonc_spline_standvedolizumab.csv
        csv_spline_standabatacept: output/data/csv_spline_standabatacept.csv
        csvhaemonc_spline_standabatacept: output/data/csvhaemonc_spline_standabatacept.csv

  run_schoenfeld:
    run: stata-mp:latest analysis/401_schoenfeld.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        logschoenfeld: logs/cox_model_diagnostics.smcl

  run_outcomes_check:
    run: r:latest analysis/outcomes_check_withandwithoutpositivetest.R
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        data1: output/data/outcomes_check.csv
  
  run_export_csv:
    run: stata-mp:latest analysis/400_export_csv.do
    needs: [run_cox_models_imid,run_cox_models_joint,run_cox_models_skin,run_cox_models_bowel,run_cox_models_imiddrugcategory,run_cox_models_standtnf,run_cox_models_standtnf3m,run_cox_models_tnfmono,run_cox_models_standil6,run_cox_models_standil17,run_cox_models_standil23,run_cox_models_standjaki,run_cox_models_standritux,run_cox_models_standinflix,run_cox_models_standvedolizumab,run_cox_models_standabatacept]
    outputs:
      moderately_sensitive:
        log: logs/export_csv.smcl
        csv_imid: output/data/csv_imid.csv
        csvhaemonc_imid: output/data/csvhaemonc_imid.csv
        csv_joint: output/data/csv_joint.csv
        csvhaemonc_joint: output/data/csvhaemonc_joint.csv
        csv_skin: output/data/csv_skin.csv
        csvhaemonc_skin: output/data/csvhaemonc_skin.csv
        csv_bowel: output/data/csv_bowel.csv
        csvhaemonc_bowel: output/data/csvhaemonc_bowel.csv
        csv_imiddrugcategory: output/data/csv_imiddrugcategory.csv
        csvhaemonc_imiddrugcategory: output/data/csvhaemonc_imiddrugcategory.csv
        csv_standtnf: output/data/csv_standtnf.csv
        csvhaemonc_standtnf: output/data/csvhaemonc_standtnf.csv
        csv_standtnf3m: output/data/csv_standtnf3m.csv
        csvhaemonc_standtnf3m: output/data/csvhaemonc_standtnf3m.csv
        csv_tnfmono: output/data/csv_tnfmono.csv
        csvhaemonc_tnfmono: output/data/csvhaemonc_tnfmono.csv
        csv_standil6: output/data/csv_standil6.csv
        csvhaemonc_standil6: output/data/csvhaemonc_standil6.csv
        csv_standil17: output/data/csv_standil17.csv
        csvhaemonc_standil17: output/data/csvhaemonc_standil17.csv
        csv_standil23: output/data/csv_standil23.csv
        csvhaemonc_standil23: output/data/csvhaemonc_standil23.csv
        csv_standjaki: output/data/csv_standjaki.csv
        csvhaemonc_standjaki: output/data/csvhaemonc_standjaki.csv
        csv_standritux: output/data/csv_standritux.csv
        csvhaemonc_standritux: output/data/csvhaemonc_standritux.csv
        csv_standinflix: output/data/csv_standinflix.csv
        csvhaemonc_standinflix: output/data/csvhaemonc_standinflix.csv
        csv_standvedolizumab: output/data/csv_standvedolizumab.csv
        csvhaemonc_standvedolizumab: output/data/csvhaemonc_standvedolizumab.csv
        csv_standabatacept: output/data/csv_standabatacept.csv
        csvhaemonc_standabatacept: output/data/csvhaemonc_standabatacept.csv

  run_forest_plots:
    run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models.R
    needs: [run_export_csv]
    outputs:
      moderately_sensitive:
        merged_csv: output/data/merged_csv_normal.csv
        merged_csv_haemoonc: output/data/merged_csv_haemonc.csv
        forest_plot_vs_gen_pop: output/figures/forest_plot_vs_gen_pop.svg
        forest_plot_vs_standard_systemic: output/figures/forest_plot_vs_standard_systemic.svg

  run_export_csv_ethnicity:
    run: stata-mp:latest analysis/600_export_csv_ethnicity.do
    needs: [run_cox_models_imid_ethnicity_1,run_cox_models_imid_ethnicity_2,run_cox_models_imid_ethnicity_3,run_cox_models_imid_ethnicity_4,run_cox_models_imid_ethnicity_5,run_cox_models_imid_ethnicity_u,run_cox_models_joint_ethnicity_1,run_cox_models_joint_ethnicity_2,run_cox_models_joint_ethnicity_3,run_cox_models_joint_ethnicity_4,run_cox_models_joint_ethnicity_5,run_cox_models_joint_ethnicity_u,run_cox_models_skin_ethnicity_1,run_cox_models_skin_ethnicity_2,run_cox_models_skin_ethnicity_3,run_cox_models_skin_ethnicity_4,run_cox_models_skin_ethnicity_5,run_cox_models_skin_ethnicity_u,run_cox_models_bowel_ethnicity_1,run_cox_models_bowel_ethnicity_2,run_cox_models_bowel_ethnicity_3,run_cox_models_bowel_ethnicity_4,run_cox_models_bowel_ethnicity_5,run_cox_models_bowel_ethnicity_u]
    outputs:
      moderately_sensitive:
        log: logs/export_csv_ethnicity.smcl
        csv_imid_ethnicity_1_csv:  output/data/csv_imid_ethnicity_1.csv
        csv_imid_ethnicity_2_csv:  output/data/csv_imid_ethnicity_2.csv
        csv_imid_ethnicity_3_csv:  output/data/csv_imid_ethnicity_3.csv
        csv_imid_ethnicity_4_csv:  output/data/csv_imid_ethnicity_4.csv
        csv_imid_ethnicity_5_csv:  output/data/csv_imid_ethnicity_5.csv
        csv_imid_ethnicity_u_csv:  output/data/csv_imid_ethnicity_u.csv
        csv_joint_ethnicity_1_csv: output/data/csv_joint_ethnicity_1.csv
        csv_joint_ethnicity_2_csv: output/data/csv_joint_ethnicity_2.csv
        csv_joint_ethnicity_3_csv: output/data/csv_joint_ethnicity_3.csv
        csv_joint_ethnicity_4_csv: output/data/csv_joint_ethnicity_4.csv
        csv_joint_ethnicity_5_csv: output/data/csv_joint_ethnicity_5.csv
        csv_joint_ethnicity_u_csv: output/data/csv_joint_ethnicity_u.csv
        csv_skin_ethnicity_1_csv:  output/data/csv_skin_ethnicity_1.csv
        csv_skin_ethnicity_2_csv:  output/data/csv_skin_ethnicity_2.csv
        csv_skin_ethnicity_3_csv:  output/data/csv_skin_ethnicity_3.csv
        csv_skin_ethnicity_4_csv:  output/data/csv_skin_ethnicity_4.csv
        csv_skin_ethnicity_5_csv:  output/data/csv_skin_ethnicity_5.csv
        csv_skin_ethnicity_u_csv:  output/data/csv_skin_ethnicity_u.csv
        csv_bowel_ethnicity_1_csv: output/data/csv_bowel_ethnicity_1.csv
        csv_bowel_ethnicity_2_csv: output/data/csv_bowel_ethnicity_2.csv
        csv_bowel_ethnicity_3_csv: output/data/csv_bowel_ethnicity_3.csv
        csv_bowel_ethnicity_4_csv: output/data/csv_bowel_ethnicity_4.csv
        csv_bowel_ethnicity_5_csv: output/data/csv_bowel_ethnicity_5.csv
        csv_bowel_ethnicity_u_csv: output/data/csv_bowel_ethnicity_u.csv
        csvhaemonc_imid_ethnicity_1_csv:  output/data/csvhaemonc_imid_ethnicity_1.csv
        csvhaemonc_imid_ethnicity_2_csv:  output/data/csvhaemonc_imid_ethnicity_2.csv
        csvhaemonc_imid_ethnicity_3_csv:  output/data/csvhaemonc_imid_ethnicity_3.csv
        csvhaemonc_imid_ethnicity_4_csv:  output/data/csvhaemonc_imid_ethnicity_4.csv
        csvhaemonc_imid_ethnicity_5_csv:  output/data/csvhaemonc_imid_ethnicity_5.csv
        csvhaemonc_imid_ethnicity_u_csv:  output/data/csvhaemonc_imid_ethnicity_u.csv
        csvhaemonc_joint_ethnicity_1_csv: output/data/csvhaemonc_joint_ethnicity_1.csv
        csvhaemonc_joint_ethnicity_2_csv: output/data/csvhaemonc_joint_ethnicity_2.csv
        csvhaemonc_joint_ethnicity_3_csv: output/data/csvhaemonc_joint_ethnicity_3.csv
        csvhaemonc_joint_ethnicity_4_csv: output/data/csvhaemonc_joint_ethnicity_4.csv
        csvhaemonc_joint_ethnicity_5_csv: output/data/csvhaemonc_joint_ethnicity_5.csv
        csvhaemonc_joint_ethnicity_u_csv: output/data/csvhaemonc_joint_ethnicity_u.csv
        csvhaemonc_skin_ethnicity_1_csv:  output/data/csvhaemonc_skin_ethnicity_1.csv
        csvhaemonc_skin_ethnicity_2_csv:  output/data/csvhaemonc_skin_ethnicity_2.csv
        csvhaemonc_skin_ethnicity_3_csv:  output/data/csvhaemonc_skin_ethnicity_3.csv
        csvhaemonc_skin_ethnicity_4_csv:  output/data/csvhaemonc_skin_ethnicity_4.csv
        csvhaemonc_skin_ethnicity_5_csv:  output/data/csvhaemonc_skin_ethnicity_5.csv
        csvhaemonc_skin_ethnicity_u_csv:  output/data/csvhaemonc_skin_ethnicity_u.csv
        csvhaemonc_bowel_ethnicity_1_csv: output/data/csvhaemonc_bowel_ethnicity_1.csv
        csvhaemonc_bowel_ethnicity_2_csv: output/data/csvhaemonc_bowel_ethnicity_2.csv
        csvhaemonc_bowel_ethnicity_3_csv: output/data/csvhaemonc_bowel_ethnicity_3.csv
        csvhaemonc_bowel_ethnicity_4_csv: output/data/csvhaemonc_bowel_ethnicity_4.csv
        csvhaemonc_bowel_ethnicity_5_csv: output/data/csvhaemonc_bowel_ethnicity_5.csv
        csvhaemonc_bowel_ethnicity_u_csv: output/data/csvhaemonc_bowel_ethnicity_u.csv

  run_export_csv_ethnicity_vs_white:
    run: stata-mp:latest analysis/601_export_csv_ethnicity_vs_white.do
    needs: [run_cox_models_genpop_ethnicity_vs_white,run_cox_models_imid_ethnicity_vs_white,run_cox_models_joint_ethnicity_vs_white,run_cox_models_skin_ethnicity_vs_white,run_cox_models_bowel_ethnicity_vs_white]
    outputs:
      moderately_sensitive:
        log: logs/export_csv_ethnicity_vs_white.smcl
        csvrun_cox_models_genpop_ethnicity_vs_white: output/data/csv_genpop_ethnicity_vs_white.csv
        csvrun_cox_models_imid_ethnicity_vs_white:   output/data/csv_imid_ethnicity_vs_white.csv
        csvrun_cox_models_joint_ethnicity_vs_white:  output/data/csv_joint_ethnicity_vs_white.csv
        csvrun_cox_models_skin_ethnicity_vs_white:   output/data/csv_skin_ethnicity_vs_white.csv
        csvrun_cox_models_bowel_ethnicity_vs_white:  output/data/csv_bowel_ethnicity_vs_white.csv

  run_forest_plots_ethnicity:
    run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models_ethnicity.R
    needs: [run_export_csv_ethnicity]
    outputs:
      moderately_sensitive:
        merged_csv_ethnicity: output/data/merged_csv_normal_ethnicity.csv
        merged_csv_haemoonc_ethnicity: output/data/merged_csv_haemonc_ethnicity.csv
        model_data_ethnicity: output/data/model_data_ethnicity.csv
        forest_plot_vs_gen_pop_ethnicity_1: output/figures/forest_plot_vs_gen_pop_ethnicity_1.svg
        forest_plot_vs_gen_pop_ethnicity_2: output/figures/forest_plot_vs_gen_pop_ethnicity_2.svg
        forest_plot_vs_gen_pop_ethnicity_3: output/figures/forest_plot_vs_gen_pop_ethnicity_3.svg
        forest_plot_vs_gen_pop_ethnicity_4: output/figures/forest_plot_vs_gen_pop_ethnicity_4.svg
        forest_plot_vs_gen_pop_ethnicity_5: output/figures/forest_plot_vs_gen_pop_ethnicity_5.svg
        forest_plot_vs_gen_pop_ethnicity_u: output/figures/forest_plot_vs_gen_pop_ethnicity_u.svg
        forest_plot_vs_gen_pop_ethnicity_died: output/figures/forest_plot_vs_gen_pop_ethnicity_died.svg
        forest_plot_vs_gen_pop_ethnicity_hospital: output/figures/forest_plot_vs_gen_pop_ethnicity_hospital.svg
        forest_plot_vs_gen_pop_ethnicity_icuordeath: output/figures/forest_plot_vs_gen_pop_ethnicity_icuordeath.svg

  run_forest_plots_ethnicity_vs_white:
    run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models_ethnicity_vs_white.R
    needs: [run_export_csv_ethnicity_vs_white]
    outputs:
      moderately_sensitive:
        merged_csv_ethnicity_vs_white: output/data/merged_csv_normal_ethnicity_vs_white.csv
        forest_plot_ethnicity_vs_white_died: output/figures/forest_plot_ethnicity_vs_white_died.svg
        forest_plot_ethnicity_vs_white_icuordeath: output/figures/forest_plot_ethnicity_vs_white_icuordeath.svg
        forest_plot_ethnicity_vs_white_hospital: output/figures/forest_plot_ethnicity_vs_white_hospital.svg

  run_merge_csvs_spline:
    run: r:latest analysis/r-immunosuppressant-meds-research/merge_csvs_spline.R
    needs: [run_spline_export_csv]
    outputs:
      moderately_sensitive:
        merged_csv_splline: output/data/merged_csv_normal_spline.csv
        merged_csv_spline_haemonc: output/data/merged_csv_haemonc_spline.csv

  run_extract_n_subjects:
    run: r:latest analysis/r-immunosuppressant-meds-research/extract_n_subjects.R
    needs: [run_cox_models_imid,run_cox_models_joint,run_cox_models_bowel,run_cox_models_skin,run_cox_models_imiddrugcategory,run_cox_models_standtnf,run_cox_models_standtnf3m,run_cox_models_tnfmono,run_cox_models_standil6,run_cox_models_standil17,run_cox_models_standil23,run_cox_models_standjaki,run_cox_models_standritux,run_cox_models_standinflix,run_cox_models_standvedolizumab,run_cox_models_standabatacept]
    outputs:
      moderately_sensitive:
        merged_csv: output/data/subject_numbers.csv

  run_pyramid_plots:
    run: stata-mp:latest analysis/602_pyramid_plots.do
    needs: [create_cohorts_single_file]
    outputs:
      moderately_sensitive:
        pyramid_plot_genpop_1: output/figures/pyramidplot_genpop_1.svg
        pyramid_plot_genpop_2: output/figures/pyramidplot_genpop_2.svg
        pyramid_plot_genpop_3: output/figures/pyramidplot_genpop_3.svg
        pyramid_plot_genpop_4: output/figures/pyramidplot_genpop_4.svg
        pyramid_plot_genpop_5: output/figures/pyramidplot_genpop_5.svg
        pyramid_plot_imid_1: output/figures/pyramidplot_imid_1.svg
        pyramid_plot_imid_2: output/figures/pyramidplot_imid_2.svg
        pyramid_plot_imid_3: output/figures/pyramidplot_imid_3.svg
        pyramid_plot_imid_4: output/figures/pyramidplot_imid_4.svg
        pyramid_plot_imid_5: output/figures/pyramidplot_imid_5.svg
        pyramid_plot_joint_1: output/figures/pyramidplot_joint_1.svg
        pyramid_plot_joint_2: output/figures/pyramidplot_joint_2.svg
        pyramid_plot_joint_3: output/figures/pyramidplot_joint_3.svg
        pyramid_plot_joint_4: output/figures/pyramidplot_joint_4.svg
        pyramid_plot_joint_5: output/figures/pyramidplot_joint_5.svg
        pyramid_plot_skin_1: output/figures/pyramidplot_skin_1.svg
        pyramid_plot_skin_2: output/figures/pyramidplot_skin_2.svg
        pyramid_plot_skin_3: output/figures/pyramidplot_skin_3.svg
        pyramid_plot_skin_4: output/figures/pyramidplot_skin_4.svg
        pyramid_plot_skin_5: output/figures/pyramidplot_skin_5.svg
        pyramid_plot_bowel_1: output/figures/pyramidplot_bowel_1.svg
        pyramid_plot_bowel_2: output/figures/pyramidplot_bowel_2.svg
        pyramid_plot_bowel_3: output/figures/pyramidplot_bowel_3.svg
        pyramid_plot_bowel_4: output/figures/pyramidplot_bowel_4.svg
        pyramid_plot_bowel_5: output/figures/pyramidplot_bowel_5.svg
        pyramid_plot_log: logs/pyramid_plots.smcl
        age_sex_summary_genpop: output/data/age_sex_summary_genpop.csv
        age_sex_summary_imid: output/data/age_sex_summary_imid.csv
        age_sex_summary_joint: output/data/age_sex_summary_joint.csv
        age_sex_summary_skin: output/data/age_sex_summary_skin.csv
        age_sex_summary_bowel: output/data/age_sex_summary_bowel.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:02:23

Config

  • Backend:
    TPP
  • Workspace:
    immunosuppressant-meds-research
  • Branch:
    master
  • Creator:
    NikNakk
  • Force run dependencies:
    False
  • Git Commit Hash:
    36a9a3c
  • Requested actions:
    • run_forest_plots
    • run_forest_plots_ethnicity
    • run_forest_plots_ethnicity_vs_white