SortMeRNA rule: minor bug and formatting

The current rule for rRNA filtering has a minor bug and could be reformatted for readability and code stability purposes.

Minor bug:

• L15: should that not happen if the OTU file is absent? The -s flag tests for an existing and non-empty file.

Formatting suggestions:

• avoid hard-coded paths
• use keywords for input/output instead of indices
• set parameters in the rule and not CMD if possible
• simplify redirection of stderr/stdout into the log file; add logs created by the tools itself
• use the option out2 to create separate PE FASTQ files instead of splitting the output later
• use temp(...) for tmp files if possible
• create unique tmp folders for working directories and clean up afterwards
• since this is the only rule, include the CMD and parameters defined above the rule into the rule itself
• add comments