Documentation on salmon decoy-aware index creation, gcbias and seqbias

[MateFlasche]

Description of feature

Requested feature
Added documentation for how the salmon index is built and whether --gcbias and --seqbias are enabled by default. If these are not enabled by default, perhaps there could be parameters for accessing them?

In the pseudo-mapping/selective alignment mode of salmon a salmon index is created. I am wondering whether, when using standard settings, the pipeline creates a decoy aware index. I am also wondering whether the complete genome is included in the as a set of decoys (SAF) or only a hard-masked version (SA).

I would appreciate documentation on this as I, and other users I'm sure, can't read code well enough to answer this myself.

Thank you for the great work!

using SAF and SA as described in
Srivastava, A., Malik, L., Sarkar, H. et al. Alignment and mapping methodology influence transcript abundance estimation. Genome Biol 21, 239 (2020).
10.1186/s13059-020-02151-8

[drpatelh]

Docs added in #913