Add in association-only flag in rule config. Add in rule evaluate to …

…complete cv-training-association-testing pipeline.
PMBio · May 2, 2024 · 45064d8 · 45064d8
1 parent 26ae231
commit 45064d8
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Showing 3 changed files with 16 additions and 5 deletions.
diff --git a/pipelines/cv_training/cv_training.snakefile b/pipelines/cv_training/cv_training.snakefile
@@ -79,8 +79,8 @@ use rule config from deeprvat_workflow as deeprvat_config with:
             for b in input.baseline
         ])  if wildcards.phenotype in training_phenotypes else ' ',
         baseline_out = lambda wildcards: f'--baseline-results-out cv_split{wildcards.cv_split}/deeprvat/{wildcards.phenotype}/deeprvat/baseline_results.parquet' if wildcards.phenotype in training_phenotypes else ' ',
-        seed_genes_out = lambda wildcards: f'--seed-genes-out cv_split{wildcards.cv_split}/deeprvat/{wildcards.phenotype}/deeprvat/seed_genes.parquet' if wildcards.phenotype in training_phenotypes else ' '
-
+        seed_genes_out = lambda wildcards: f'--seed-genes-out cv_split{wildcards.cv_split}/deeprvat/{wildcards.phenotype}/deeprvat/seed_genes.parquet' if wildcards.phenotype in training_phenotypes else ' ',
+        association_only = lambda wildcards: f'--association-only' if wildcards.phenotype not in training_phenotypes else ' '
 
 
 

diff --git a/pipelines/cv_training/cv_training_association_testing.snakefile b/pipelines/cv_training/cv_training_association_testing.snakefile
@@ -33,14 +33,21 @@ wildcard_constraints:
 cv_splits = config.get("n_folds", 5)
 cv_exp = True
 
-
-
 include: "cv_training.snakefile"
 include: "cv_burdens.snakefile"
 include: "../association_testing/burdens.snakefile"
 include: "../association_testing/regress_eval.snakefile"
 
 
+rule all_evaluate:  #regress_eval.snakefile
+    input:
+        significant=expand(
+            "{phenotype}/deeprvat/eval/significant.parquet", phenotype=phenotypes
+        ),
+        results=expand(
+            "{phenotype}/deeprvat/eval/all_results.parquet", phenotype=phenotypes
+        ),
+
 
 rule all_regression:  #regress_eval.snakefile
     input:

diff --git a/pipelines/training/config.snakefile b/pipelines/training/config.snakefile
@@ -33,11 +33,15 @@ rule config:
         baseline_out=lambda wildcards: f"--baseline-results-out  {wildcards.phenotype}/deeprvat/baseline_results.parquet"
         if wildcards.phenotype in training_phenotypes
         else " ",
+        association_only=lambda wildcards: f"--association-only"
+        if wildcards.phenotype not in training_phenotypes
+        else " ",
     shell:
         (
             "deeprvat_config update-config "
             "--phenotype {wildcards.phenotype} "
-            "{params.baseline_results}"
+            "{params.association_only} "
+            "{params.baseline_results} "
             "{params.baseline_out} "
             "{params.seed_genes_out} "
             "{input.config} "