Remove ERDS reference affecting wgs_cnv_annotation (#257)

bihealth · Nov 30, 2022 · 57ce889 · 57ce889
1 parent f6aedfc
commit 57ce889
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Showing 2 changed files with 9 additions and 19 deletions.
diff --git a/snappy_pipeline/workflows/wgs_cnv_annotation/__init__.py b/snappy_pipeline/workflows/wgs_cnv_annotation/__init__.py
@@ -114,27 +114,18 @@ def get_input_files(self, action):
         def input_function(wildcards):
             # Validate action
             self._validate_action(action)
-
-            # TODO: make work for non-ERDS/ERDS+SV2
+            # Pedigree file
             tpl = "work/write_pedigree.{index_ngs_library}/out/{index_ngs_library}.ped"
             yield "ped", tpl.format(**wildcards)
+            # SVs
+            key_ext = {"vcf": ".vcf.gz", "tbi": ".vcf.gz.tbi"}
             tpl = (
-                "work/{mapper}.{caller}.{index_ngs_library}/out/"
+                "output/{mapper}.{caller}.{index_ngs_library}/out/"
                 "{mapper}.{caller}.{index_ngs_library}"
             )
-            if wildcards.caller.startswith("erds"):
-                key_ext = {"vcf": ".vcf.gz", "tbi": ".vcf.gz.tbi"}
-            else:
-                key_ext = {"vcf": ".bcf", "tbi": ".bcf.csi"}
-            # SVs
             wgs_cnv_calling = self.parent.sub_workflows["wgs_cnv_calling"]
-            if wildcards.caller == "erds_sv2":
-                tpl = tpl.replace(".{index_ngs_library}", ".merge_genotypes")
-            elif not wildcards.caller.startswith("erds"):
-                tpl = tpl.replace(".{index_ngs_library}", ".merge_genotypes")
             for key, ext in key_ext.items():
                 yield key, wgs_cnv_calling(tpl + ext).format(**wildcards)
-            return
 
         return input_function
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_annotation.py
@@ -38,14 +38,13 @@ def minimal_config():
 
           wgs_cnv_calling:
             variant_calling_tool: gatk_ug
-            tools:
-            - erds_sv2
+            tools: [delly2, gcnv]
 
           wgs_cnv_annotation:
             path_ngs_mapping: ../ngs_mapping
             path_wgs_cnv_calling: ../wgs_cnv_calling
             tools_ngs_mapping: [bwa]
-            tools_wgs_cnv_calling: [erds_sv2]
+            tools_wgs_cnv_calling: [delly2, gcnv]
 
         data_sets:
           first_batch:
@@ -95,11 +94,11 @@ def wgs_cnv_annotation_workflow(
 def test_vcf_cnv_filter_step_part_get_input_files(wgs_cnv_annotation_workflow):
     """Tests VcfCnvFilterStepPart.get_input_files()"""
     wildcards = Wildcards(
-        fromdict={"mapper": "bwa", "index_ngs_library": "P001-N1-DNA1-WGS1", "caller": "erds_sv2"}
+        fromdict={"mapper": "bwa", "index_ngs_library": "P001-N1-DNA1-WGS1", "caller": "delly2"}
     )
     # Define expected
     wgs_cnv_calling_path = (
-        "WGS_CNV_CALLING/work/bwa.erds_sv2.merge_genotypes/out/bwa.erds_sv2.merge_genotypes"
+        "WGS_CNV_CALLING/output/bwa.delly2.P001-N1-DNA1-WGS1/out/bwa.delly2.P001-N1-DNA1-WGS1"
     )
     expected = {
         "ped": "work/write_pedigree.P001-N1-DNA1-WGS1/out/P001-N1-DNA1-WGS1.ped",
@@ -164,7 +163,7 @@ def test_wgs_cnv_annotation_workflow(wgs_cnv_annotation_workflow):
         for i in (1, 4)
         for ext in ("vcf.gz", "vcf.gz.md5", "vcf.gz.tbi", "vcf.gz.tbi.md5")
         for mapper in ("bwa",)
-        for cnv_caller in ("erds_sv2",)
+        for cnv_caller in ("delly2", "gcnv")
     ]
     expected = list(sorted(expected))
     actual = list(sorted(wgs_cnv_annotation_workflow.get_result_files()))