Capture stdout from Clair3

[mwhamgenomics]

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]

This is a good point. I shall add it to the list of to dos :-)