generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: "3.0"
expectations:
population_size: 100000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
W2_generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_W2
outputs:
highly_sensitive:
cohort: output/input_W2.csv
01_hhClassif_cr_analysis_dataset:
run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do MAIN
needs: [generate_cohort]
outputs:
highly_sensitive:
allHHSizes: output/allHH_beforeDropping_largerThan10_MAIN.dta
allHHSizes1_20: output/allHH_sizedBetween1And20_MAIN.dta
allvars: output/hhClassif_analysis_datasetMAIN.dta
allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityMAIN.dta
allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*MAIN.dta
allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*MAIN.dta
moderately_sensitive:
log: logs/01_hhClassif_cr_analysis_dataset.log
01_hhClassif_cr_analysis_dataset_W2:
run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do W2
needs: [W2_generate_cohort]
outputs:
highly_sensitive:
allHHSizes: output/allHH_beforeDropping_largerThan10_W2.dta
allHHSizes1_20: output/allHH_sizedBetween1And20_W2.dta
allvars: output/hhClassif_analysis_datasetW2.dta
allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityW2.dta
allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*W2.dta
allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*W2.dta
moderately_sensitive:
log: logs/01_hhClassif_cr_analysis_dataset_W2.log
02_hhClassif_an_data_checks:
run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
moderately_sensitive:
log: logs/02_hhClassif_an_data_checks.log
02_hhClassif_an_data_checks_W2:
run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do W2
needs: [01_hhClassif_cr_analysis_dataset_W2]
outputs:
moderately_sensitive:
log: logs/02_hhClassif_an_data_checks_W2.log
03a_hhClassif_an_hist_hhSizebyEthnicity:
run: stata-mp:latest analysis/03a_hhClassif_an_hist_hhSizebyEthnicity.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
moderately_sensitive:
log: logs/03a_hhClassif_an_hist_hhSizebyEthnicity_MAIN.log
gph1: output/overallHHSizeDist_MAIN.gph
gph2: output/whiteHHSizeDist_MAIN.gph
gph3: output/southAsianHHSizeDist_MAIN.gph
gph4: output/blackHHSizeDist_MAIN.gph
gph5: output/HHdistHists_MAIN.pdf
03b_hhClassif_an_hist_ov65hhSizebyEthnicity:
run: stata-mp:latest analysis/03b_hhClassif_an_hist_ov65hhSizebyEthnicity.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
moderately_sensitive:
log: logs/03b_hhClassif_an_hist_ov65hhSizebyEthnicity_MAIN.log
gph1: output/ov65OverallHHSizeDist_MAIN.gph
gph2: output/ov65WhiteHHSizeDist_MAIN.gph
gph3: output/ov65SouthAsianHHSizeDist_MAIN.gph
gph4: output/ov65BlackHHSizeDist_MAIN.gph
gph5: output/ov65HHdistHists_MAIN.pdf
03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge:
run: stata-mp:latest analysis/03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
highly_sensitive:
over65OnlyHH: output/housesWithOnly65yrOldsInThem_MAIN.dta
moderately_sensitive:
log: logs/03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge_MAIN.log
gph1: output/ov65OverallHHSizeDist_woAllSameAge_MAIN.gph
gph2: output/ov65WhiteHHSizeDist_woAllSameAge_MAIN.gph
gph3: output/ov65SouthAsianHHSizeDist_woAllSameAge_MAIN.gph
gph4: output/ov65BlackHHSizeDist_woAllSameAge_MAIN.gph
gph5: output/ov65HHdistHists_woAllSameAge_MAIN.pdf
03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban:
run: stata-mp:latest analysis/03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
moderately_sensitive:
log: logs/03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban_MAIN.log
gph1: output/ov65OverallHHSizeDist_*_MAIN.gph
gph2: output/ov65WhiteHHSizeDist_*_MAIN.gph
gph3: output/ov65SouthAsianHHSizeDist_*_MAIN.gph
gph4: output/ov65BlackHHSizeDist_*_MAIN.gph
gph5: output/ov65HHdistHists_*_MAIN.pdf
03e_hhClassif_an_descriptive_table_1:
run: stata-mp:latest analysis/03e_hhClassif_an_descriptive_table_1.do MAIN
needs: [01_hhClassif_cr_analysis_dataset]
outputs:
moderately_sensitive:
log: logs/03e_hhClassif_an_descriptive_table_1_MAIN.log
tableTxt: output/table1_hhClassifMAIN.txt
tableExcel: output/table1_hhClassifMAIN.xlsx
03e_hhClassif_an_descriptive_table_1_W2:
run: stata-mp:latest analysis/03e_hhClassif_an_descriptive_table_1.do W2
needs: [01_hhClassif_cr_analysis_dataset_W2]
outputs:
moderately_sensitive:
log: logs/03e_hhClassif_an_descriptive_table_1_W2.log
tableTxt: output/table1_hhClassifW2.txt
tableExcel: output/table1_hhClassifW2.xlsx
04_hhClassif_an_univariable_analysis:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do MAIN
outputs:
moderately_sensitive:
log: logs/04_hhClassif_an_univariable_analysis_MAIN.log
data: output/hhClassif_univariableAnalysis_*_ageband_*MAIN.ster
04_hhClassif_an_univariable_analysis_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do W2
outputs:
moderately_sensitive:
log: logs/04_hhClassif_an_univariable_analysis_W2.log
data: output/hhClassif_univariableAnalysis_*_ageband_*W2.ster
05_hhClassif_an_multivariable_analysis:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do MAIN
outputs:
moderately_sensitive:
log: logs/05_hhClassif_an_multivariable_analysis_MAIN.log
data: output/hhClassif_multivariableAllEthnicities_*_ageband_*MAIN.ster
05_hhClassif_an_multivariable_analysis_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do W2
outputs:
moderately_sensitive:
log: logs/05_hhClassif_an_multivariable_analysis_W2.log
data: output/hhClassif_multivariableAllEthnicities_*_ageband_*W2.ster
06_hhClassif_an_multivariable_analysis_eth5Interaction:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do MAIN
outputs:
moderately_sensitive:
log: logs/06_hhClassif_an_eth5Interaction_analysis_MAIN.log
06_hhClassif_an_multivariable_analysis_eth5Interaction_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do W2
outputs:
moderately_sensitive:
log: logs/06_hhClassif_an_eth5Interaction_analysis_W2.log
07_hhClassif_an_multivariable_analysis_perEth5Group:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do MAIN
outputs:
moderately_sensitive:
log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_MAIN.log
data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*MAIN.ster
07_hhClassif_an_multivariable_analysis_perEth5Group_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do W2
outputs:
moderately_sensitive:
log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_W2.log
data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*W2.ster
08_hhClassif_an_mv_analysis_perEth5Group_HR_table:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/08_hhClassif_an_mv_analysis_perEth5Group_HR_table.do MAIN
outputs:
moderately_sensitive:
# log1: logs/08_hhClassif_tablecontent_HRtable_covidDeath_MAIN.log
# log2: logs/08_hhClassif_tablecontent_HRtable_covidHosp_MAIN.log
log3: logs/08_hhClassif_tablecontent_HRtable_covidHospOrDeath_MAIN.log
# log4: logs/08_hhClassif_tablecontent_HRtable_nonCovidDeath_MAIN.log
# table1: output/hhClassif_tablecontents_HRtable_covidDeath_MAIN.txt
# table2: output/hhClassif_tablecontents_HRtable_covidHosp_MAIN.txt
table3: output/hhClassif_tablecontents_HRtable_covidHospOrDeath_MAIN.txt
# table4: output/hhClassif_tablecontents_HRtable_nonCovidDeath_MAIN.txt
08_hhClassif_an_mv_analysis_perEth5Group_HR_table_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/08_hhClassif_an_mv_analysis_perEth5Group_HR_table.do W2
outputs:
moderately_sensitive:
# log1: logs/08_hhClassif_tablecontent_HRtable_covidDeath_W2.log
# log2: logs/08_hhClassif_tablecontent_HRtable_covidHosp_W2.log
log3: logs/08_hhClassif_tablecontent_HRtable_covidHospOrDeath_W2.log
# log4: logs/08_hhClassif_tablecontent_HRtable_nonCovidDeath_W2.log
# table1: output/hhClassif_tablecontents_HRtable_covidDeath_W2.txt
# table2: output/hhClassif_tablecontents_HRtable_covidHosp_W2.txt
table3: output/hhClassif_tablecontents_HRtable_covidHospOrDeath_W2.txt
# table4: output/hhClassif_tablecontents_HRtable_nonCovidDeath_W2.txt
09_hhClassif_an_mv_analysis_perEth16Group_HR_table:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/09_hhClassif_an_mv_analysis_perEth16Group_HR_table.do MAIN
outputs:
moderately_sensitive:
# log1: logs/09_hhClassif_tablecontent_HRtable_eth16_covidDeath_MAIN.log
# log2: logs/09_hhClassif_tablecontent_HRtable_eth16_covidHosp_MAIN.log
log3: logs/09_hhClassif_tablecontent_HRtable_eth16_covidHospOrDeath_MAIN.log
# log4: logs/09_hhClassif_tablecontent_HRtable_eth16_nonCovidDeath_MAIN.log
# table1: output/hhClassif_tablecontents_HRtable_eth16_covidDeath_MAIN.txt
# table2: output/hhClassif_tablecontents_HRtable_eth16_covidHosp_MAIN.txt
table3: output/hhClassif_tablecontents_HRtable_eth16_covidHospOrDeath_MAIN.txt
# table4: output/hhClassif_tablecontents_HRtable_eth16_nonCovidDeath_MAIN.txt
09_hhClassif_an_mv_analysis_perEth16Group_HR_table_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/09_hhClassif_an_mv_analysis_perEth16Group_HR_table.do W2
outputs:
moderately_sensitive:
# log1: logs/09_hhClassif_tablecontent_HRtable_eth16_covidDeath_W2.log
# log2: logs/09_hhClassif_tablecontent_HRtable_eth16_covidHosp_W2.log
log3: logs/09_hhClassif_tablecontent_HRtable_eth16_covidHospOrDeath_W2.log
# log4: logs/09_hhClassif_tablecontent_HRtable_eth16_nonCovidDeath_W2.log
# table1: output/hhClassif_tablecontents_HRtable_eth16_covidDeath_W2.txt
# table2: output/hhClassif_tablecontents_HRtable_eth16_covidHosp_W2.txt
table3: output/hhClassif_tablecontents_HRtable_eth16_covidHospOrDeath_W2.txt
# table4: output/hhClassif_tablecontents_HRtable_eth16_nonCovidDeath_W2.txt
10_hh_imd_descriptives_W1:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/10_hh_imd_descriptives_W1.do
outputs:
moderately_sensitive:
log: logs/10_eth_imd_descriptives_W1.log
table: output/table_ethnicity_descriptivesMAIN.txt
11_hhClassif_an_mv_perEth5Group_HR_3CATSFULLMVtable:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/11_hhClassif_an_mv_perEth5Group_HR_3CATSFULLMVtable.do MAIN
outputs:
moderately_sensitive:
# log1: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidDeath_MAIN.log
# log2: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidHosp_MAIN.log
log3: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidHospOrDeath_MAIN.log
# log4: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_nonCovidDeath_MAIN.log
# table1: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidDeath_MAIN.txt
#table2: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidHosp_MAIN.txt
table3: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidHospOrDeath_MAIN.txt
# table4: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_nonCovidDeath_MAIN.txt
11_hhClassif_an_mv_perEth5Group_HR_3CATSFULLMVtable_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/11_hhClassif_an_mv_perEth5Group_HR_3CATSFULLMVtable.do W2
outputs:
moderately_sensitive:
# log1: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidDeath_W2.log
# log2: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidHosp_W2.log
log3: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_covidHospOrDeath_W2.log
# log4: logs/hhClassif_tablecontent_HR_3CATSFULLMVtable_nonCovidDeath_W2.log
# table1: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidDeath_W2.txt
# table2: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidHosp_W2.txt
table3: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_covidHospOrDeath_W2.txt
# table4: output/hhClassif_tablecontents_HRtable_3CATSFULLMVtable_nonCovidDeath_W2.txt
#
12_hhClassif_an_MV_analysis_W_SA_multipleInteractions:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/12_hhClassif_an_MV_analysis_W_SA_multipleInteractions.do MAIN
outputs:
moderately_sensitive:
log: logs/12_hhClassif_an_MV_analysis_W_SA_multipleinteractions_MAIN.log
12_hhClassif_an_MV_analysis_W_SA_multipleinteractions_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/12_hhClassif_an_MV_analysis_W_SA_multipleInteractions.do W2
outputs:
moderately_sensitive:
log: logs/12_hhClassif_an_MV_analysis_W_SA_multipleinteractions_W2.log
13_hhClassif_an_MV_analysis_test_for_trend:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/13_hhClassif_an_MV_analysis_test_for_trend.do MAIN
outputs:
moderately_sensitive:
log: logs/13_hhClassif_an_MV_analysis_test_for_trend_MAIN.log
13_hhClassif_an_MV_analysis_test_for_trend_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/13_hhClassif_an_MV_analysis_test_for_trend.do W2
outputs:
moderately_sensitive:
log: logs/13_hhClassif_an_MV_analysis_test_for_trend_W2.log
14_hhClassif_an_MV_analyses_p_values_for_var_associations:
needs: [01_hhClassif_cr_analysis_dataset]
run: stata-mp:latest analysis/14_hhClassif_an_MV_analyses_p_values_for_var_associations.do MAIN
outputs:
moderately_sensitive:
log: logs/14_hhClassif_an_MV_analyses_p_values_for_var_associations_MAIN.log
14_hhClassif_an_MV_analyses_p_values_for_var_associations_W2:
needs: [01_hhClassif_cr_analysis_dataset_W2]
run: stata-mp:latest analysis/14_hhClassif_an_MV_analyses_p_values_for_var_associations.do W2
outputs:
moderately_sensitive:
log: logs/14_hhClassif_an_MV_analyses_p_values_for_var_associations_W2.log