project.yaml

### CTV3, PRIMIS, SNOMED analysis

version: '3.0'

expectations:
  population_size: 1000

actions:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data: codelists/ethnicity_*.csv

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_5 --output-file output/extract_5/input_5.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_5/input_5.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_5:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_5/input_5.feather
        --output-dir output/extract_5
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_5/input_5.html

  generate_study_population_16:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_16 --output-file output/extract_16/input_16.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_16/input_16.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_16:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_16/input_16.feather
        --output-dir output/extract_16
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_16/input_16.html

  generate_study_population_time:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_time --output-file output/extract_time/input_time.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_time/input_time.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_time:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_time/input_time.feather
        --output-dir output/extract_time
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_time/input_time.html

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/5_group/tables/*.csv

  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/16_group/tables/simpl*.csv


######## SUS
  execute_simple_validation_analyses_sus:
    run: python:latest python analysis/sus/simple_validation_script_sus.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/5_group/tables/*.csv
#        figures: output/sus/simplified_output/5_group/figures/*.png

  execute_simple_validation_analyses_ctv3_sus:
    run: python:latest python analysis/sus/simple_validation_script_ctv3_sus.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/5_group/tables/*ctv3*.csv
#        figures: output/sus/simplified_output/5_group/figures/*.png

  execute_simple_validation_analyses_16_sus:
    run: python:latest python analysis/sus/simple_validation_script_16_sus.py
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/16_group/tables/simpl*.csv


################## over time

  time_tables:
    run: r:latest analysis/time/times.R
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        data: output/time/*.csv
        plots: output/time/*.png

  monthly_ethnicity_nulldates_1990:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1990-01-01 to 1990-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_years*.feather

  monthly_ethnicity_nulldates_1991:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1991-01-01 to 1991-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_year*.feather

  monthly_ethnicity_nulldates_1992:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1992-01-01 to 1992-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_yea*.feather

  monthly_ethnicity_nulldates_1993:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1993-01-01 to 1993-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_ye*.feather

  monthly_ethnicity_nulldates_1994:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1994-01-01 to 1994-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_y*.feather

  monthly_ethnicity_nulldates_1995:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1995-01-01 to 1995-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures_*.feather

  monthly_ethnicity_nulldates_1996:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1996-01-01 to 1996-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measures*.feather

  monthly_ethnicity_nulldates_1997:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1997-01-01 to 1997-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measure*.feather

  monthly_ethnicity_nulldates_1998:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1998-01-01 to 1998-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measur*.feather

  monthly_ethnicity_nulldates_1999:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '1999-01-01 to 1999-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_measu*.feather

  monthly_ethnicity_nulldates_2000:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2000-01-01 to 2000-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_meas*.feather

  monthly_ethnicity_nulldates_2001:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2001-01-01 to 2001-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_mea*.feather

  monthly_ethnicity_nulldates_2002:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2002-01-01 to 2002-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_me*.feather

  monthly_ethnicity_nulldates_2003:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2003-01-01 to 2003-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_m*.feather

  monthly_ethnicity_nulldates_2004:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2004-01-01 to 2004-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities_*.feather

  monthly_ethnicity_nulldates_2005:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2005-01-01 to 2005-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicities*.feather

  monthly_ethnicity_nulldates_2006:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2006-01-01 to 2006-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicitie*.feather

  monthly_ethnicity_nulldates_2007:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2007-01-01 to 2007-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethniciti*.feather

  monthly_ethnicity_nulldates_2008:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2008-01-01 to 2008-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnicit*.feather

  monthly_ethnicity_nulldates_2009:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2009-01-01 to 2009-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnici*.feather

  monthly_ethnicity_nulldates_2010:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2010-01-01 to 2010-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethnic*.feather

  monthly_ethnicity_nulldates_2011:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2011-01-01 to 2011-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethni*.feather

  monthly_ethnicity_nulldates_2012:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2012-01-01 to 2012-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_ethn*.feather

  monthly_ethnicity_nulldates_2013:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2013-01-01 to 2013-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_eth*.feather

  monthly_ethnicity_nulldates_2014:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2014-01-01 to 2014-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_et*.feather

  monthly_ethnicity_nulldates_2015:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2015-01-01 to 2015-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_e*.feather

  monthly_ethnicity_nulldates_2016:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2016-01-01 to 2016-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates_*.feather

  monthly_ethnicity_nulldates_2017:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2017-01-01 to 2017-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldates*.feather

  monthly_ethnicity_nulldates_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2018-01-01 to 2018-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldate*.feather

  monthly_ethnicity_nulldates_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2019-01-01 to 2019-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulldat*.feather

  monthly_ethnicity_nulldates_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2020-01-01 to 2020-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nullda*.feather

  monthly_ethnicity_nulldates_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2021-01-01 to 2021-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nulld*.feather

  monthly_ethnicity_nulldates_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2022-01-01 to 2022-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_null*.feather

  monthly_ethnicity_nulldates_2023:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2023-01-01 to 2023-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nul*.feather

  monthly_ethnicity_nulldates_2024:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nulldates_ethnicities_measures_years
        --index-date-range '2024-01-01 to 2024-01-01 by month' --output-dir=output/yearly/nulldates
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/yearly/nulldates/input_nu*.feather

  monthly_nulldates_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_nulldates_ethnicities_measures_years --output-dir=output/yearly/nulldates
    needs:
    - monthly_ethnicity_nulldates_1990
    - monthly_ethnicity_nulldates_1991
    - monthly_ethnicity_nulldates_1992
    - monthly_ethnicity_nulldates_1993
    - monthly_ethnicity_nulldates_1994
    - monthly_ethnicity_nulldates_1995
    - monthly_ethnicity_nulldates_1996
    - monthly_ethnicity_nulldates_1997
    - monthly_ethnicity_nulldates_1998
    - monthly_ethnicity_nulldates_1999
    - monthly_ethnicity_nulldates_2000
    - monthly_ethnicity_nulldates_2001
    - monthly_ethnicity_nulldates_2002
    - monthly_ethnicity_nulldates_2003
    - monthly_ethnicity_nulldates_2004
    - monthly_ethnicity_nulldates_2005
    - monthly_ethnicity_nulldates_2006
    - monthly_ethnicity_nulldates_2007
    - monthly_ethnicity_nulldates_2008
    - monthly_ethnicity_nulldates_2009
    - monthly_ethnicity_nulldates_2010
    - monthly_ethnicity_nulldates_2011
    - monthly_ethnicity_nulldates_2012
    - monthly_ethnicity_nulldates_2013
    - monthly_ethnicity_nulldates_2014
    - monthly_ethnicity_nulldates_2015
    - monthly_ethnicity_nulldates_2016
    - monthly_ethnicity_nulldates_2017
    - monthly_ethnicity_nulldates_2018
    - monthly_ethnicity_nulldates_2019
    - monthly_ethnicity_nulldates_2020
    - monthly_ethnicity_nulldates_2021
    - monthly_ethnicity_nulldates_2022
    - monthly_ethnicity_nulldates_2023
    - monthly_ethnicity_nulldates_2024
    outputs:
      moderately_sensitive:
        measure_csv: output/yearly/nulldates/measure_*.csv

#### Yearly ethnicities
  monthly_ethnicity_1990:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1990-01-01 to 1990-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_years*.feather
          
  monthly_ethnicity_1991:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1991-01-01 to 1991-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_year*.feather
          
  monthly_ethnicity_1992:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1992-01-01 to 1992-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_yea*.feather

          
  monthly_ethnicity_1993:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1993-01-01 to 1993-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_ye*.feather
          
  monthly_ethnicity_1994:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1994-01-01 to 1994-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_y*.feather

          
  monthly_ethnicity_1995:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1995-01-01 to 1995-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures_*.feather

          
  monthly_ethnicity_1996:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1996-01-01 to 1996-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measures*.feather

          
  monthly_ethnicity_1997:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1997-01-01 to 1997-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measure*.feather

          
  monthly_ethnicity_1998:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1998-01-01 to 1998-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measur*.feather

          
  monthly_ethnicity_1999:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '1999-01-01 to 1999-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_measu*.feather


  monthly_ethnicity_2000:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2000-01-01 to 2000-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_meas*.feather


  monthly_ethnicity_2001:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2001-01-01 to 2001-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_mea*.feather

        
  monthly_ethnicity_2002:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2002-01-01 to 2002-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_me*.feather


        
  monthly_ethnicity_2003:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2003-01-01 to 2003-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_m*.feather


        
  monthly_ethnicity_2004:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2004-01-01 to 2004-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities_*.feather


        
  monthly_ethnicity_2005:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2005-01-01 to 2005-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicities*.feather
      
  monthly_ethnicity_2006:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2006-01-01 to 2006-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicitie*.feather


        
  monthly_ethnicity_2007:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2007-01-01 to 2007-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethniciti*.feather


        
  monthly_ethnicity_2008:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2008-01-01 to 2008-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnicit*.feather
      
  monthly_ethnicity_2009:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2009-01-01 to 2009-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnici*.feather
      
  monthly_ethnicity_2010:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2010-01-01 to 2010-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethnic*.feather


        
  monthly_ethnicity_2011:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2011-01-01 to 2011-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethni*.feather


        
  monthly_ethnicity_2012:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2012-01-01 to 2012-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_ethn*.feather


        
  monthly_ethnicity_2013:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2013-01-01 to 2013-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_eth*.feather


        
  monthly_ethnicity_2014:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2014-01-01 to 2014-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_et*.feather


        
  monthly_ethnicity_2015:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2015-01-01 to 2015-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_e*.feather

        
  monthly_ethnicity_2016:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2016-01-01 to 2016-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly_*.feather

        
  monthly_ethnicity_2017:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2017-01-01 to 2017-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthly*.feather

  monthly_ethnicity_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2018-01-01 to 2018-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_monthl*.feather
      
  monthly_ethnicity_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2019-01-01 to 2019-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_month*.feather
      
  monthly_ethnicity_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2020-01-01 to 2020-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_mont*.feather
      
  monthly_ethnicity_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2021-01-01 to 2021-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_mon*.feather
      
  monthly_ethnicity_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2022-01-01 to 2022-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_mo*.feather
      
  monthly_ethnicity_2023:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2023-01-01 to 2023-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_m*.feather

        
  monthly_ethnicity_2024:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly_ethnicities_measures_years
        --index-date-range '2024-01-01 to 2024-01-01 by month' --output-dir=output/yearly
        --output-format=feather
    needs:
    - split_codelist
    outputs:
      highly_sensitive:
        extract: output/yearly/input_*.feather
     
  monthly_ethnicity_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_monthly_ethnicities_measures_years --output-dir=output/yearly
    needs:
    - monthly_ethnicity_1990
    - monthly_ethnicity_1991
    - monthly_ethnicity_1992
    - monthly_ethnicity_1993
    - monthly_ethnicity_1994
    - monthly_ethnicity_1995
    - monthly_ethnicity_1996
    - monthly_ethnicity_1997
    - monthly_ethnicity_1998
    - monthly_ethnicity_1999
    - monthly_ethnicity_2000
    - monthly_ethnicity_2001
    - monthly_ethnicity_2002
    - monthly_ethnicity_2003
    - monthly_ethnicity_2004
    - monthly_ethnicity_2005
    - monthly_ethnicity_2006
    - monthly_ethnicity_2007
    - monthly_ethnicity_2008
    - monthly_ethnicity_2009
    - monthly_ethnicity_2010
    - monthly_ethnicity_2011
    - monthly_ethnicity_2012
    - monthly_ethnicity_2013
    - monthly_ethnicity_2014
    - monthly_ethnicity_2015
    - monthly_ethnicity_2016
    - monthly_ethnicity_2017
    - monthly_ethnicity_2018
    - monthly_ethnicity_2019
    - monthly_ethnicity_2020
    - monthly_ethnicity_2021
    - monthly_ethnicity_2022
    - monthly_ethnicity_2023
    - monthly_ethnicity_2024
    - split_codelist
    outputs:
      moderately_sensitive:
        measure_csv: output/yearly/measure_*.csv

  time_rate_plots:
    run: r:latest analysis/time/time_covariate_plots.R
    needs: 
      - monthly_ethnicity_measures
      - monthly_nulldates_measures
    outputs:
      moderately_sensitive:
        data: output/time/*rate.csv
        plots: output/time/*rate.png

  report_tables:
    run: python:latest python analysis/report_tables.py
    needs: [execute_simple_validation_analyses_16_sus, execute_simple_validation_analyses_ctv3_sus,execute_simple_validation_analyses_sus,execute_simple_validation_analyses,execute_simple_validation_analyses_16]
    outputs:
      moderately_sensitive: 
        tables: output/report_tables/*.csv

  generate_ons_comparisons:
    run: r:latest analysis/sus/combine_ons_sus.R
    needs: [execute_simple_validation_analyses_16_sus,execute_simple_validation_analyses_sus]
    outputs:
      moderately_sensitive:
        csvs: output/sus/simplified_output/*/tables/ethnic_group*.csv

##### draft report
  generate_draft_report_rmd:
    run: r:latest -e 'rmarkdown::render("notebooks_r/report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/report")'
    needs: [generate_ons_comparisons,report_tables, execute_simple_validation_analyses,execute_simple_validation_analyses_16,execute_simple_validation_analyses_sus,execute_simple_validation_analyses_16_sus]
    outputs:
      moderately_sensitive:
        html: output/report/report.html

#### move released files to output/released
###### run locally for manuscript
##### local notebook
  generate_local_runs:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/local_runs.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
    outputs:
      moderately_sensitive:
        csvs: output/released/made_locally/*.csv

  # process_ons_census_data:
  #   run: r:latest analysis/local/ons_process.R
  #   outputs:
  #     moderately_sensitive:
  #       csvs: data/*.csv.gz

  # generate_local_ons_comparisons:
  #   run: r:latest analysis/local/combine_ons_sus.R
  #   needs: [process_ons_census_data]
  #   outputs:
  #     moderately_sensitive:
  #       csvs: output/released/made_locally/ethnic_group*.csv
  #       tests: output/tests/*.csv

## create outputs for the manuscript
  ## library(hrbrthemes) not currently available on the OS R image
  # generate_manuscript_plots:
  #   run: r:latest analysis/local/local_manuscript_plots.R
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/released/made_locally/*.png

## create outputs for the appendix
# `row_group.as_column = TRUE` option not currently available on the OS R image
  # generate_appendix:
  #   run: r:latest analysis/local/appendix.R
  #   needs: [generate_local_runs]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/released/made_locally/*.html
  #       pdf: output/released/made_locally/*.pdf