Port SalmonTE part into 3t-seq

[ftabaro]

The SalmonTE analysis is currently implemented a standard set of rules executing that tool as standard CLI tool. However, The SalmonTE program is implemented as a Snakemake pipeline decorated with a command-line interface and downstream functions that produce summary statistics and plots. In its current version the tool has zero dependencies management. This forced me to write a Docker container to encapsulate them and add it as dependency of 3t-seq.

With this feature request I would like to start porting SalmonTE into 3t-seq to polish it and streamline dependency management and remove 3t-seq dependency from SalmonTE Docker image.

I envision this feature as a porting of SalmonTE Snakefile(s) and its extension with additional rules covering the extra steps downstream of Salmon quantification.

For reference, this is the original SalmonTE repository: https://github.com/hyunhwan-jeong/SalmonTE