Mark output files with pipeline modifiers

[epruesse]

E.g. overriding default trimming length should be marked on output file name to avoid confusion. It's documented inside files, but file and would be useful.

[epruesse]

This referrs to the files copied into the PipelineResults folder. Currently, using different trimming lengths (for example) is not added to the report name, so it's only visible after opening the RDS file, or not really visible at all.