From e28f8737c29892ae0f6f27da9fa4d2f5f2e4b11a Mon Sep 17 00:00:00 2001 From: Kayla Meyer Date: Wed, 9 Oct 2024 08:28:44 +0200 Subject: [PATCH] Reset default of center_scale_burdens to True --- pipelines/association_testing_pretrained.snakefile | 2 +- pipelines/association_testing_pretrained_regenie.snakefile | 2 +- pipelines/training_association_testing.snakefile | 2 +- pipelines/training_association_testing_regenie.snakefile | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pipelines/association_testing_pretrained.snakefile b/pipelines/association_testing_pretrained.snakefile index a2fb82a0..96bd08ac 100644 --- a/pipelines/association_testing_pretrained.snakefile +++ b/pipelines/association_testing_pretrained.snakefile @@ -13,7 +13,7 @@ training_phenotypes = [] n_burden_chunks = config.get('n_burden_chunks', 1) if not debug_flag else 2 n_regression_chunks = config.get('n_regression_chunks', 40) if not debug_flag else 2 n_avg_chunks = config.get('n_avg_chunks', 1) -center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', False) else '' +center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', True) else '' n_trials = config['hyperparameter_optimization']['n_trials'] n_bags = config['training']['n_bags'] if not debug_flag else 3 n_repeats = config['n_repeats'] diff --git a/pipelines/association_testing_pretrained_regenie.snakefile b/pipelines/association_testing_pretrained_regenie.snakefile index d6e32574..2ec5f923 100644 --- a/pipelines/association_testing_pretrained_regenie.snakefile +++ b/pipelines/association_testing_pretrained_regenie.snakefile @@ -13,7 +13,7 @@ training_phenotypes = [] n_burden_chunks = config.get('n_burden_chunks', 1) if not debug_flag else 2 n_regression_chunks = config.get('n_regression_chunks', 40) if not debug_flag else 2 n_avg_chunks = config.get('n_avg_chunks', 1) -center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', False) else '' +center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', True) else '' n_bags = config['training']['n_bags'] if not debug_flag else 3 n_repeats = config['n_repeats'] debug = '--debug ' if debug_flag else '' diff --git a/pipelines/training_association_testing.snakefile b/pipelines/training_association_testing.snakefile index 34f86176..cf6a20fa 100644 --- a/pipelines/training_association_testing.snakefile +++ b/pipelines/training_association_testing.snakefile @@ -17,7 +17,7 @@ training_phenotypes = list(training_phenotypes.keys()) if type(training_phenotyp n_burden_chunks = config.get('n_burden_chunks', 1) if not debug_flag else 2 n_regression_chunks = config.get('n_regression_chunks', 40) if not debug_flag else 2 n_avg_chunks = config.get('n_avg_chunks', 1) -center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', False) else '' +center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', True) else '' n_trials = config['hyperparameter_optimization']['n_trials'] n_bags = config['training']['n_bags'] if not debug_flag else 3 n_repeats = config['n_repeats'] diff --git a/pipelines/training_association_testing_regenie.snakefile b/pipelines/training_association_testing_regenie.snakefile index 535a63a9..66c8b179 100644 --- a/pipelines/training_association_testing_regenie.snakefile +++ b/pipelines/training_association_testing_regenie.snakefile @@ -16,7 +16,7 @@ training_phenotypes = list(training_phenotypes.keys()) if type(training_phenotyp n_burden_chunks = config.get('n_burden_chunks', 1) if not debug_flag else 2 n_regression_chunks = config.get('n_regression_chunks', 40) if not debug_flag else 2 n_avg_chunks = config.get('n_avg_chunks', 1) -center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', False) else '' +center_scale_burdens = '--center-scale-burdens ' if config.get('center_scale_burdens', True) else '' n_trials = config['hyperparameter_optimization']['n_trials'] n_bags = config['training']['n_bags'] if not debug_flag else 3 n_repeats = config['n_repeats']