Add decoy-aware indexing for salmon

[j-andrews7]

salmon performs best when using a decoy-aware transcriptome. The salmon docs explain pretty clearly how this can be done, but I will advise that the partial decoy transcriptome generation via the generateDecoyTranscriptome.sh script is very resource intensive and rather finicky.

Generating the full decoy transcriptome file is more straightforward, though the resulting index is quite large and it's memory-intensive to generate. This latter method would be quite straightforward to add to the pipeline. In short, it really only requires concatenation of transcriptome/genome sequences and snagging the genome target names to use as decoys in the indexing step via -d.

Alternatively, this could be added after refgenie is adopted, as they maintain pre-made indices as well.

[j-andrews7]

For posterity, also note that salmon can quantify aligned bams as well.

[drpatelh]

Decoy support as well as the ability to use salmon quant on BAM files has been added in #526