Fixed inconsistent configuration dict usage in _yield_peddy_results()

bihealth · Aug 8, 2022 · ede0509 · ede0509
1 parent c6ca7fd
commit ede0509
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/snappy_pipeline/workflows/variant_checking/__init__.py b/snappy_pipeline/workflows/variant_checking/__init__.py
@@ -209,15 +209,15 @@ def _yield_peddy_results(self):
                 for path in self.sub_steps["peddy"].get_output_files("run").values():
                     yield from expand(
                         path,
-                        mapper=self.config["tools_ngs_mapping"]["dna"],
+                        mapper=self.config["tools_ngs_mapping"],
                         var_caller=self.config["tools_variant_calling"],
                         index_ngs_library=[pedigree.index.dna_ngs_library.name],
                     )
         if "gatk_hc_gvcf" in self.config["tools_variant_calling"]:
             for path in self.sub_steps["peddy"].get_output_files("run").values():
                 yield from expand(
                     path,
-                    mapper=self.config["tools_ngs_mapping"]["dna"],
+                    mapper=self.config["tools_ngs_mapping"],
                     var_caller=["gatk_hc_gvcf"],
                     index_ngs_library=["whole_cohort"],
                 )

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_checking.py b/tests/snappy_pipeline/workflows/test_workflows_variant_checking.py
@@ -35,6 +35,12 @@ def minimal_config():
             tools:
             - gatk_hc
 
+          variant_checking:
+            tools_ngs_mapping: ['bwa']  # optional, copied from ngs mapping config
+            tools_variant_calling: ['gatk_hc']  # optional, copied from variant calling config
+            path_variant_calling: ../variant_calling  # REQUIRED
+            tools: ['peddy']
+
         data_sets:
           first_batch:
             file: sheet.tsv