Merge pull request #369 from genomic-medicine-sweden/Smeds-patch-2

fix: change from svdb_query file to svdb_merge file
genomic-medicine-sweden · Nov 24, 2023 · 6c9cd90 · 6c9cd90
2 parents 5ec38a8 + 1ed29ad
commit 6c9cd90
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/rules/common_references.smk b/workflow/rules/common_references.smk
@@ -129,7 +129,7 @@ def get_gvcfs(units: pandas.DataFrame, name: str) -> typing.List[str]:
 
 
 def get_cnv_vcfs(units: pandas.DataFrame, name: str) -> typing.List[str]:
-    return get_files(units, name, "cnv_sv/svdb_query/%s_%s.pathology_purecn.svdb_query.vcf")
+    return get_files(units, name, "cnv_sv/svdb_merge/%s_%s.pathology_purecn.merged.vcf")
 
 
 def get_cnvkit_target(units: pandas.DataFrame, name: str) -> typing.List[str]: