Cleanup module configs and decide on default output files

We should really cleanup our module config. It can be heavily simplified. For most of the modules we only add a config to export log files?
We could add a function to add the log files based on a parameter (e.g. write_logs_to_outdir). I only added this in the beginning for CI actually. Not sure if this is really needed. You also get the logs in the .command.out of the work dirs when debugging locally.

While we are doing that, we should decide on the default outputs of the pipeline. What do we really want to have in the outdir per default? I would say just the mzTab/MSstats/parquet files and the things needed for the report.