Check for specific analysis output mode when deciding whether to analyze run

[dfornika]

If we want to re-analyze a run, we typically delete (or move) the original analysis outputs for that run. Then when the system scans again it will see that there is a set of fastq files available for a run that have not been analyzed.

But there may be cases where we want to specifically re-run either the short-only or the hybrid analysis, without interfering with any other existing analyses for the run. In that case, the system should check for the output directory of the specific analysis mode and re-run the analysis for that mode if it doesn't exist.