Software versions section in report should filter out tools not used

[andersgs]

In Nullarbor report, all the tool dependencies and their versions are listed. But, these include multiple assemblers, multiple species kmer-based identifiers, multiple tree building tools. It then becomes hard to know which ones were actually used.

[tseemann]

I will have to add a new section to the report for this.

However if you use --prefill this week not be true information, because the user can patch in heterogeneous data sources.