From dfebe7724e27522faa12dd18b7be495732efb12c Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Thu, 9 Mar 2023 13:36:16 +0100
Subject: [PATCH] fix: fix to snappy varfish-upload (#158)

---
 cubi_tk/snappy/varfish_upload.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/cubi_tk/snappy/varfish_upload.py b/cubi_tk/snappy/varfish_upload.py
index 08db615c..4fecd889 100644
--- 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",