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