From cb10dbbcedd9e9d287428f14873420c5b6d4898c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolai=20von=20K=C3=BCgelgen?=
 <nicolai.von-kuegelgen@bih-charite.de>
Date: Fri, 26 Jan 2024 13:17:10 +0100
Subject: [PATCH] fix: varfish cli 06x uses new import syntax (#220) (#222)

---
 cubi_tk/snappy/varfish_upload.py | 4 ++--
 requirements/base.txt            | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/cubi_tk/snappy/varfish_upload.py b/cubi_tk/snappy/varfish_upload.py
index fd7bebb..17c851b 100644
--- a/cubi_tk/snappy/varfish_upload.py
+++ b/cubi_tk/snappy/varfish_upload.py
@@ -4,11 +4,11 @@
 import glob
 import os
 import pathlib
+from subprocess import check_call
 import typing
 
 from biomedsheets import shortcuts
 from logzero import logger
-from varfish_cli.__main__ import main as varfish_cli_main
 
 from ..common import find_base_path
 from .common import load_sheet_tsv
@@ -284,7 +284,7 @@ def _process_dataset(self, ds: DataSet):
                 answer = answer_str == "y"
             if answer:
                 logger.info("Executing '%s'", " ".join(args))
-                varfish_cli_main(args[1:])
+                check_call(args)
         logger.info("  -> all done with %s", name)
 
 
diff --git a/requirements/base.txt b/requirements/base.txt
index 4e62737..0d59aed 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -52,7 +52,7 @@ argcomplete
 pyyaml
 
 # VarFish REST API client.
-varfish-cli >=0.6.2,<=0.7.0
+varfish-cli >=0.6.2,<0.7.0
 
 # Compact, round-tripable configuration format.
 toml