Added missing argument to targeted_seq_cnv_export #241

bihealth · Nov 11, 2022 · a8b3d24 · a8b3d24
1 parent fde704d
commit a8b3d24
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Showing 2 changed files with 19 additions and 1 deletion.
diff --git a/snappy_pipeline/workflows/targeted_seq_cnv_export/__init__.py b/snappy_pipeline/workflows/targeted_seq_cnv_export/__init__.py
@@ -86,6 +86,7 @@
     path_refseq_ser: REQUIRED    # REQUIRED: path to RefSeq .ser file
     path_ensembl_ser: REQUIRED   # REQUIRED: path to ENSEMBL .ser file
     path_db: REQUIRED            # REQUIRED: spath to annotator DB file to use
+    varfish_server_compatibility: false # OPTIONAL: build output compatible with varfish-server v1.2 (Anthenea) and early versions of the v2 (Bollonaster)
 """
 
 
@@ -214,7 +215,11 @@ def get_params(self, action):
         assert action == "annotate"
 
         def get_params_func(wildcards):
-            result = {"is_wgs": False, "step_name": "targeted_seq_cnv_export"}
+            result = {
+                "is_wgs": False,
+                "step_name": "targeted_seq_cnv_export",
+                "varfish_server_compatibility": self.config["varfish_server_compatibility"],
+            }
             pedigree = self.index_ngs_library_to_pedigree[wildcards.index_ngs_library]
             for donor in pedigree.donors:
                 if (

diff --git a/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_export.py b/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_export.py
@@ -5,6 +5,7 @@
 
 import pytest
 import ruamel.yaml as ruamel_yaml
+from snakemake.io import Wildcards
 
 from snappy_pipeline.workflows.targeted_seq_cnv_export import TargetedSeqCnvExportWorkflow
 
@@ -143,6 +144,18 @@ def test_varfish_annotator_step_part_get_log_file(targeted_seq_cnv_export_workfl
     assert actual == expected
 
 
+def test_varfish_annotator_step_part_get_params_annotate(targeted_seq_cnv_export_workflow):
+    """Tests VarfishAnnotatorAnnotateStepPart._get_params_annotate()"""
+    wildcards = Wildcards(fromdict={"index_ngs_library": "P001-N1-DNA1-WGS1"})
+    expected = {
+        "is_wgs": True,
+        "step_name": "targeted_seq_cnv_export",
+        "varfish_server_compatibility": False,
+    }
+    actual = targeted_seq_cnv_export_workflow.get_params("varfish_annotator", "annotate")(wildcards)
+    assert actual == expected
+
+
 def test_varfish_annotator_step_part_get_resource_usage(targeted_seq_cnv_export_workflow):
     """Tests VarfishAnnotatorAnnotateStepPart.get_resource_usage()"""
     # Define expected