Merge branch 'hjulienn-master-patch-84798' into 'master'

- Correct naming of custom loadings in create_wk

See merge request !111

jass/__main__.py

@@ -143,16 +143,17 @@ def compute_worktable(args):
     pos_Start = args.start_position
     pos_End = args.end_position
 
-    if args.omnibus:
-        strategy = "jass.models.stats:omnibus_stat"
-    elif args.sumz:
+  
+    if args.sumz:
         strategy = "jass.models.stats:sumz_stat"
     elif args.fisher_test:
         strategy = "jass.models.stats:fisher_test"
     elif args.meta_analysis:
         strategy = "jass.models.stats:meta_analysis"
     else:
-        strategy = args.strategy
+        strategy = "jass.models.stats:omnibus_stat"
+    #elif args.strategy is not None:
+    #    strategy = args.strategy
 
     create_worktable_file(
         phenotype_ids=selected_phenotypes,
@@ -169,7 +170,7 @@ def compute_worktable(args):
         chromosome=chromosome,
         pos_Start=pos_Start,
         pos_End=pos_End,
-        custom_loadings=custom_loadings,
+        loadings=custom_loadings,
     )
 
 
@@ -400,7 +401,6 @@ def get_parser():
     strategies.add_argument("--sumz", action="store_true", default=False)
     strategies.add_argument("--fisher_test", action="store_true", default=False)
     strategies.add_argument("--meta_analysis", action="store_true", default=False)
-    strategies.add_argument("--strategy")
 
     parser_create_pd.set_defaults(func=w_create_project_data)
 
@@ -533,7 +533,6 @@ def get_parser():
     strategies.add_argument("--sumz", action="store_true", default=False)
     strategies.add_argument("--fisher_test", action="store_true", default=False)
     strategies.add_argument("--meta_analysis", action="store_true", default=False)
-    strategies.add_argument("--strategy")
 
     parser_create_wt.set_defaults(func=w_create_worktable)