fix: fix to snappy varfish-upload (#158)

bihealth · Mar 9, 2023 · dfebe77 · dfebe77
1 parent 6284db9
commit dfebe77
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/cubi_tk/snappy/varfish_upload.py b/cubi_tk/snappy/varfish_upload.py
@@ -24,6 +24,7 @@
     "wgs_cnv_export_external",
     "wgs_sv_export",
     "wgs_sv_export_external",
+    "varfish_export",
 )
 
 #: The extensions that we are looking for.
@@ -37,6 +38,7 @@
     "bwa.gcnv",
     "bwa.popdel",
     "bwa.xhmm",
+    "bwa_mem2.varfish_",
     "minimap2.sniffles2",
     "write_pedigree",
 )
@@ -264,6 +266,7 @@ def _process_dataset(self, ds: DataSet):
             # Perform call to varfish import.
             args = [
                 "varfish-cli",
+                "--no-verify-ssl",
                 "--verbose",
                 "case",
                 "create-import-info",