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feat: allow varfish case resubmission #224

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merged 6 commits into from
Feb 8, 2024
Merged

feat: allow varfish case resubmission #224

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1055c7f
fix: adapt to varfish-cli >=0.6.2 syntax
Nicolai-vKuegelgen Jan 26, 2024
7e45c38
fix: adapt to varfish-cli >=0.6.2 syntax
Nicolai-vKuegelgen Jan 26, 2024
0678372
Merge branch 'main' into 220-varfish-cli-06x-uses-new-import-syntax
Nicolai-vKuegelgen Jan 26, 2024
a087efc
linting
Nicolai-vKuegelgen Jan 26, 2024
d9286fb
Merge branch 'main' of github.com:bihealth/cubi-tk
Nicolai-vKuegelgen Jan 26, 2024
a95a7de
Feat: allow cubi-tk to force varfish case resubmission
Nicolai-vKuegelgen Feb 8, 2024
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8 changes: 8 additions & 0 deletions cubi_tk/snappy/varfish_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,13 @@ def setup_argparse(cls, parser: argparse.ArgumentParser) -> None:
required=False,
help="Assume yes to all answers",
)
parser.add_argument(
"--force-resubmit",
"-f",
action="store_true",
required=False,
help="Force re-submission of exitsing cases in varfish.",
)
parser.add_argument(
"--samples",
help=(
Expand Down Expand Up @@ -271,6 +278,7 @@ def _process_dataset(self, ds: DataSet):
"--verbose",
"importer",
"caseimportinfo-create",
"--resubmit" if self.args.force_resubmit else "",
sodar_uuid,
*sorted(found.values()),
]
Expand Down
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