Reset default of center_scale_burdens to True

PMBio · Oct 9, 2024 · e28f873 · e28f873
1 parent ccc5d56
commit e28f873
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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']