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Capture stdout from Clair3 #78

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mwhamgenomics opened this issue Dec 18, 2024 · 1 comment
Open

Capture stdout from Clair3 #78

mwhamgenomics opened this issue Dec 18, 2024 · 1 comment
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@mattloose
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enhancement New feature or request

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@mwhamgenomics
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At the moment, Robin runs Clair3 via Docker/os.system. As a result, we get stdout and errors from Clair3 in the terminal but not in the log file. Can we log the stdout from the Docker call, e.g. with subprocess.check_output or subprocess.Popen?
@mattloose mattloose added the enhancement New feature or request label Dec 18, 2024
@mattloose
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This is a good point. I shall add it to the list of to dos :-)

@mattloose mattloose self-assigned this Dec 18, 2024
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