pipeline bugfixes and renamings

PMBio · Feb 22, 2024 · e42b478 · e42b478
1 parent 6acdcf4
commit e42b478
Show file tree

Hide file tree

Showing 5 changed files with 6 additions and 9 deletions.
diff --git a/example/config.yaml b/example/config.yaml
@@ -26,7 +26,7 @@ alpha: 0.05
 
 n_burden_chunks: 2
 n_regression_chunks: 2
-n_avg_chunks: 2
+n_avg_chunks: 1
 
 n_repeats: 2
 

diff --git a/pipelines/association_testing/burdens.snakefile b/pipelines/association_testing/burdens.snakefile
@@ -67,7 +67,7 @@ rule compute_burdens:
     input:
         reversed = model_path / "reverse_finished.tmp",
         checkpoints = lambda wildcards: [
-            model_path / f'repeat_{repeat}/best/bag_{bag}.ckpt'
+            f'{model_path}/repeat_{repeat}/best/bag_{bag}.ckpt'
             for repeat in range(n_repeats) for bag in range(n_bags)
         ],
         dataset = '{phenotype}/deeprvat/association_dataset.pkl',
@@ -82,7 +82,6 @@ rule compute_burdens:
         mem_mb = 2000000,        # Using this value will tell our modified lsf.profile not to set a memory resource
         load = 8000,
         gpus = 1
-
     shell:
         ' && '.join([
             ('deeprvat_associate compute-burdens '

diff --git a/pipelines/association_testing/regress_eval.snakefile b/pipelines/association_testing/regress_eval.snakefile
@@ -1,6 +1,7 @@
 config_file_prefix = (
     "cv_split0/deeprvat/" if cv_exp else ""
 )  
+########### Average regression 
 rule evaluate:
     input:
         associations ='{phenotype}/deeprvat/average_regression_results/burden_associations.parquet',

diff --git a/pipelines/association_testing_pretrained.snakefile b/pipelines/association_testing_pretrained.snakefile
@@ -22,7 +22,6 @@ wildcard_constraints:
     repeat="\d+",
     trial="\d+",
 
-<<<<<<< HEAD
 cv_exp = False
 config_file_prefix = (
     "cv_split0/deeprvat/" if cv_exp else ""

diff --git a/pipelines/cv_training/cv_training_association_testing.snakefile b/pipelines/cv_training/cv_training_association_testing.snakefile
@@ -32,9 +32,7 @@ wildcard_constraints:
 
 cv_splits = config.get("n_folds", 5)
 cv_exp = True
-# config_file_prefix = (
-#     "cv_split0/deeprvat/" if cv_exp else ""
-# )  # needed in case we analyse a CV experiment
+
 
 
 include: "../association_testing/plot.snakefile"
@@ -51,7 +49,7 @@ rule all_plot:  #plot.snakefile
         "dicovery_replication_plot.png",
 
 
-rule all_evaluate_avg:  #plot.snakefile
+rule all_evaluate:  #plot.snakefile
     input:
         significant=expand(
             "{phenotype}/deeprvat/eval/significant.parquet", phenotype=phenotypes
@@ -61,7 +59,7 @@ rule all_evaluate_avg:  #plot.snakefile
         ),
 
 
-rule all_regression_avg:  #regress_eval_avg.snakefile
+rule all_regression:  #regress_eval.snakefile
     input:
         expand(
             "{phenotype}/deeprvat/average_regression_results/burden_associations.parquet",