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.
L15: should that not happen if the OTU file is absent? The
-sflag tests for an existing and non-empty file.
- 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
out2to create separate PE FASTQ files instead of splitting the output later
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