Unify SummarizedExperiment output

[grst]

Description of feature

Currently, the pipeline generates three SummarizedExperiment .rds files while it would be more convenient and less confusing to generate a single one with different assay layers.

Current situation

There are three rds files:

All of which have a counts and abundance layer

The abundance layer is the same in all three objects

While the counts are different representing counts, length scaled counts and scaled counts, respectively.

Proposed solution

Create a single SummarizedExperiment with the following assays:

• tpm (what is currently in "abundance", but the name is more explicit)
• counts
• counts_scaled
• counts_length_scaled
• gene_lengths (what is currently in salmon.merged.gene_lengths.tsv)

possibly, it could be worth adding a vst layer generated by DESeq2::vst().

Create another one for the transcripts with the same layers.

[grst]

@drpatelh would you accept a PR for this?