Separate STDOUT & STDERR streams in Snakemake rules

Currently, the STDOUT and STDERR output streams of most (all?) rules in the workflow are redirected to a single file per rule. As some rules write data to these streams that may be used by another rule downstream, this approach can lead to problems. In order to have a consistent style for all rules and because it is not always obvious/foreseeable which output may be used downstream in the future, all rules should redirect STDOUT and STDERR streams to separate files, following a clear naming convention.