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SW-961: Log stderr but do not use it as output to parse. Unfortunately, slurm...

Jan David Mol requested to merge SW-961-fix-pipelinecontrol-2 into master

SW-961: Log stderr but do not use it as output to parse. Unfortunately, slurm seems to give stderr output we occasionally have to ignore. If we need to ever check stderr, we may need a filter.

Closes SW-961

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