From c5223370e9c88a84b469c95c77b0f446d48f6530 Mon Sep 17 00:00:00 2001 From: Em Prestige Date: Fri, 20 Sep 2024 08:05:43 +0100 Subject: [PATCH] update yaml --- actions.txt | 2 +- create-project.R | 6 +++--- project.yaml | 24 ++++++++++++------------ 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/actions.txt b/actions.txt index 2c94e04..709f912 100644 --- a/actions.txt +++ b/actions.txt @@ -23,5 +23,5 @@ phenotype_sensitivity_older_adults_s1 phenotype_sensitivity_older_adults_s2 phen phenotype_sensitivity_adults_s1 phenotype_sensitivity_adults_s2 phenotype_sensitivity_adults_s3 phenotype_sensitivity_adults_s4 phenotype_sensitivity_adults_s5 phenotype_sensitivity_adults_s6 phenotype_sensitivity_adults_s7 phenotype_sensitivity_children_and_adolescents_s1 phenotype_sensitivity_children_and_adolescents_s2 phenotype_sensitivity_children_and_adolescents_s3 phenotype_sensitivity_children_and_adolescents_s4 phenotype_sensitivity_children_and_adolescents_s5 phenotype_sensitivity_children_and_adolescents_s6 phenotype_sensitivity_children_and_adolescents_s7 phenotype_sensitivity_infants_s1 phenotype_sensitivity_infants_s2 phenotype_sensitivity_infants_s3 phenotype_sensitivity_infants_s4 phenotype_sensitivity_infants_s5 phenotype_sensitivity_infants_s6 phenotype_sensitivity_infants_s7 -collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_older_adults collate_rsv_model_outputs_tables_older_adults collate_flu_model_outputs_tables_older_adults collate_covid_model_outputs_tables_older_adults collate_overall_and_all_cause_model_outputs_tables_older_adults collate_rsv_sensitivity_model_outputs_tables_older_adults collate_flu_sensitivity_model_outputs_tables_older_adults collate_covid_sensitivity_model_outputs_tables_older_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults collate_phenotype_sensitivity_tables_older_adults collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_model_outputs_tables_adults collate_rsv_sensitivity_model_outputs_tables_adults collate_flu_sensitivity_model_outputs_tables_adults collate_covid_sensitivity_model_outputs_tables_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults collate_phenotype_sensitivity_tables_adults collate_flow_chart_tables_children_and_adolescents collate_table1_tables_children_and_adolescents collate_rates_tables_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_children_and_adolescents collate_rsv_model_outputs_tables_children_and_adolescents collate_flu_model_outputs_tables_children_and_adolescents collate_covid_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents collate_flu_sensitivity_model_outputs_tables_children_and_adolescents collate_covid_sensitivity_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents collate_phenotype_sensitivity_tables_children_and_adolescents collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_infants collate_rsv_model_outputs_tables_infants collate_flu_model_outputs_tables_infants collate_covid_model_outputs_tables_infants collate_overall_and_all_cause_model_outputs_tables_infants collate_rsv_sensitivity_model_outputs_tables_infants collate_flu_sensitivity_model_outputs_tables_infants collate_covid_sensitivity_model_outputs_tables_infants collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants collate_phenotype_sensitivity_tables_infants +collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_older_adults collate_rsv_model_outputs_tables_older_adults collate_flu_model_outputs_tables_older_adults collate_covid_model_outputs_tables_older_adults collate_overall_and_all_cause_model_outputs_tables_older_adults collate_rsv_sensitive_model_outputs_tables_older_adults collate_flu_sensitive_model_outputs_tables_older_adults collate_covid_sensitivity_model_outputs_tables_older_adults collate_overall_and_all_cause_sensitive_model_outputs_tables_older_adults collate_phenotype_sensitivity_tables_older_adults collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_model_outputs_tables_adults collate_rsv_sensitive_model_outputs_tables_adults collate_flu_sensitive_model_outputs_tables_adults collate_covid_sensitivity_model_outputs_tables_adults collate_overall_and_all_cause_sensitive_model_outputs_tables_adults collate_phenotype_sensitivity_tables_adults collate_flow_chart_tables_children_and_adolescents collate_table1_tables_children_and_adolescents collate_rates_tables_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_children_and_adolescents collate_rsv_model_outputs_tables_children_and_adolescents collate_flu_model_outputs_tables_children_and_adolescents collate_covid_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents collate_rsv_sensitive_model_outputs_tables_children_and_adolescents collate_flu_sensitive_model_outputs_tables_children_and_adolescents collate_covid_sensitivity_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_sensitive_model_outputs_tables_children_and_adolescents collate_phenotype_sensitivity_tables_children_and_adolescents collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_infants collate_rsv_model_outputs_tables_infants collate_flu_model_outputs_tables_infants collate_covid_model_outputs_tables_infants collate_overall_and_all_cause_model_outputs_tables_infants collate_rsv_sensitive_model_outputs_tables_infants collate_flu_sensitive_model_outputs_tables_infants collate_covid_sensitivity_model_outputs_tables_infants collate_overall_and_all_cause_sensitive_model_outputs_tables_infants collate_phenotype_sensitivity_tables_infants diff --git a/create-project.R b/create-project.R index 0499f2f..263a332 100644 --- a/create-project.R +++ b/create-project.R @@ -1670,7 +1670,7 @@ action_finalise <- function(cohort) { ), action( - name = glue("collate_rsv_sensitivity_model_outputs_tables_{cohort}"), + name = glue("collate_rsv_sensitive_model_outputs_tables_{cohort}"), run = glue("r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R {cohort}"), arguments = c(cohort), needs = list(glue("analyse_dataset_{cohort}_rsv_ethnicity_s1_sensitive_primary"), @@ -1727,7 +1727,7 @@ action_finalise <- function(cohort) { ), action( - name = glue("collate_flu_sensitivity_model_outputs_tables_{cohort}"), + name = glue("collate_flu_sensitive_model_outputs_tables_{cohort}"), run = glue("r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R {cohort}"), arguments = c(cohort), needs = list(glue("analyse_dataset_{cohort}_flu_ethnicity_s1_sensitive_primary"), @@ -1820,7 +1820,7 @@ action_finalise <- function(cohort) { ), action( - name = glue("collate_overall_and_all_cause_sensitivity_model_outputs_tables_{cohort}"), + name = glue("collate_overall_and_all_cause_sensitive_model_outputs_tables_{cohort}"), run = glue("r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R {cohort}"), arguments = c(cohort), needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s1_sensitive_primary"), diff --git a/project.yaml b/project.yaml index bd3c3de..3bce019 100644 --- a/project.yaml +++ b/project.yaml @@ -44064,7 +44064,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/older_adults_overall_and_all_cause_model_outputs_collated.csv - collate_rsv_sensitivity_model_outputs_tables_older_adults: + collate_rsv_sensitive_model_outputs_tables_older_adults: run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R older_adults older_adults needs: @@ -44121,7 +44121,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/older_adults_rsv_sensitivity_model_outputs_collated.csv - collate_flu_sensitivity_model_outputs_tables_older_adults: + collate_flu_sensitive_model_outputs_tables_older_adults: run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R older_adults older_adults needs: @@ -44214,7 +44214,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/older_adults_covid_sensitivity_model_outputs_collated.csv - collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults: + collate_overall_and_all_cause_sensitive_model_outputs_tables_older_adults: run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R older_adults older_adults needs: @@ -44566,7 +44566,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/adults_overall_and_all_cause_model_outputs_collated.csv - collate_rsv_sensitivity_model_outputs_tables_adults: + collate_rsv_sensitive_model_outputs_tables_adults: run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R adults adults needs: @@ -44623,7 +44623,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/adults_rsv_sensitivity_model_outputs_collated.csv - collate_flu_sensitivity_model_outputs_tables_adults: + collate_flu_sensitive_model_outputs_tables_adults: run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R adults adults needs: @@ -44716,7 +44716,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/adults_covid_sensitivity_model_outputs_collated.csv - collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults: + collate_overall_and_all_cause_sensitive_model_outputs_tables_adults: run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R adults adults needs: @@ -45070,7 +45070,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv - collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents: + collate_rsv_sensitive_model_outputs_tables_children_and_adolescents: run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: @@ -45127,7 +45127,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/children_and_adolescents_rsv_sensitivity_model_outputs_collated.csv - collate_flu_sensitivity_model_outputs_tables_children_and_adolescents: + collate_flu_sensitive_model_outputs_tables_children_and_adolescents: run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: @@ -45220,7 +45220,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/children_and_adolescents_covid_sensitivity_model_outputs_collated.csv - collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents: + collate_overall_and_all_cause_sensitive_model_outputs_tables_children_and_adolescents: run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: @@ -45572,7 +45572,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/infants_overall_and_all_cause_model_outputs_collated.csv - collate_rsv_sensitivity_model_outputs_tables_infants: + collate_rsv_sensitive_model_outputs_tables_infants: run: r:latest analysis/collation_code/rsv_sensitivity_model_outputs_table_collation.R infants infants needs: @@ -45629,7 +45629,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/infants_rsv_sensitivity_model_outputs_collated.csv - collate_flu_sensitivity_model_outputs_tables_infants: + collate_flu_sensitive_model_outputs_tables_infants: run: r:latest analysis/collation_code/flu_sensitivity_model_outputs_table_collation.R infants infants needs: @@ -45722,7 +45722,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/infants_covid_sensitivity_model_outputs_collated.csv - collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants: + collate_overall_and_all_cause_sensitive_model_outputs_tables_infants: run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R infants infants needs: