fix: varfish cli 06x uses new import syntax (#220) (#222)

bihealth · Jan 26, 2024 · cb10dbb · cb10dbb
1 parent 9619609
commit cb10dbb
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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