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qbic-pipelines / querynator

MIT License
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query-api-civic: unknown param 'cancer' #33

Closed HomoPolyethylen closed 2 weeks ago

HomoPolyethylen commented 3 weeks ago

Description of the bug

sth went wrong during the last release (0.5.0), query-api-civic is broken.

Command used and terminal output

querynator query-api-civic     --vcf test_sample.normalized.vcf.gz     --outdir test_sample_civic --cancer foo

                                           __ 
  ____ ___  _____  _______  ______  ____ _/ /_____  _____
 / __ `/ / / / _ \/ ___/ / / / __ \/ __ `/ __/ __ \/ ___/
/ /_/ / /_/ /  __/ /  / /_/ / / / / /_/ / /_/ /_/ / /
\__, /\__,_/\___/_/   \__, /_/ /_/\__,_/\__/\____/_/
  /_/                /____/

2024-07-02 10:42:36,693 - Querynator - INFO - Start
Traceback (most recent call last):
  File "/home/casimir/opt/miniforge3/envs/qn/bin/querynator", line 10, in <module>
    sys.exit(run_querynator())
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/querynator/__main__.py", line 278, in run_querynator
    querynator_cli()
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/casimir/opt/miniforge3/envs/qn/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
TypeError: query_api_civic() got an unexpected keyword argument 'cancer'

System information

No response