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Sample_qc - check input arguments #49

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ellendejong opened this issue Aug 20, 2021 · 0 comments
Open

Sample_qc - check input arguments #49

ellendejong opened this issue Aug 20, 2021 · 0 comments

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@ellendejong
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I tried to use sample_qc with only specifying a sample and not a panel.
branch develop

python ExonCov.py sample_qc -s 141

Expected behaviour

Message from argument parser, not all required parameters provided.

Observed behaviour

TypeError.

Traceback (most recent call last):
  File "ExonCov.py", line 29, in <module>
    manager.run()
  File "/hpc/diaggen/software/development/ExonCov/venv/lib/python2.7/site-packages/flask_script/__init__.py", line 417, in run
    result = self.handle(argv[0], argv[1:])
  File "/hpc/diaggen/software/development/ExonCov/venv/lib/python2.7/site-packages/flask_script/__init__.py", line 386, in handle
    res = handle(*args, **config)
  File "/hpc/diaggen/software/development/ExonCov/venv/lib/python2.7/site-packages/flask_script/commands.py", line 216, in __call__
    return self.run(*args, **kwargs)
  File "/hpc/diaggen/software/development/ExonCov/ExonCov/cli.py", line 349, in run
    if len(samples) != len(panels):
TypeError: <ExonCov.cli.SampleQC object at 0x2ae89c546650>: object of type 'NoneType' has no len()
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