improve modularity

PMBio · Apr 11, 2024 · dd41088 · dd41088
1 parent b964fda
commit dd41088
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Showing 2 changed files with 26 additions and 4 deletions.
diff --git a/pipelines/association_testing/regress_eval.snakefile b/pipelines/association_testing/regress_eval.snakefile
@@ -1,7 +1,29 @@
+configfile: 'config.yaml'
+
+debug_flag = config.get('debug', False)
+debug = '--debug ' if debug_flag else ''
+
+phenotypes = config['phenotypes']
+phenotypes = list(phenotypes.keys()) if type(phenotypes) == dict else 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', 40)
+
+do_scoretest = '--do-scoretest ' if config.get('do_scoretest', False) else ''
+
+cv_exp = config.get("cv_exp", False)
 config_file_prefix = (
     "cv_split0/deeprvat/" if cv_exp else ""
 )  
 ########### Average regression 
+rule all_evaluate:
+    input:
+        expand("{phenotype}/deeprvat/eval/significant.parquet",
+               phenotype=phenotypes),
+        expand("{phenotype}/deeprvat/eval/all_results.parquet",
+               phenotype=phenotypes),
+
 rule evaluate:
     input:
         associations ='{phenotype}/deeprvat/average_regression_results/burden_associations.parquet',

diff --git a/pipelines/association_testing/regress_eval_regenie.snakefile b/pipelines/association_testing/regress_eval_regenie.snakefile
@@ -76,8 +76,8 @@ rule regenie_step2:
         bgen = "regenie_input/deeprvat_pseudovariants.bgen",
         covariate_file = "regenie_input/covariates.txt",
         phenotype_file = "regenie_input/phenotypes.txt",
-        step1_loco = expand("regenie_output/step1/deeprvat_{pheno_num}.loco",
-                            pheno_num=range(1, len(phenotypes) + 1)),
+        # step1_loco = expand("regenie_output/step1/deeprvat_{pheno_num}.loco",
+        #                     pheno_num=range(1, len(phenotypes) + 1)),
         step1_predlist = "regenie_output/step1/deeprvat_pred.list"
         # step1_loco = expand("regenie_output/step1/deeprvat_l1_{pheno_number}.loco",
         #                     pheno_number=range(len(phenotypes))),
@@ -110,8 +110,8 @@ rule regenie_step1:
         covariate_file = "regenie_input/covariates.txt",
         phenotype_file = "regenie_input/phenotypes.txt",
     output:
-        expand("regenie_output/step1/deeprvat_{pheno_num}.loco",
-               pheno_num=range(1, len(phenotypes) + 1)),
+        # expand("regenie_output/step1/deeprvat_{pheno_num}.loco",
+        #        pheno_num=range(1, len(phenotypes) + 1)),
         "regenie_output/step1/deeprvat_pred.list"
     threads: 24
     resources: