Turn off quantification flag

[adamrtalbot]

Description of feature

There isn't currently a method of producing a BAM file without performing quantification, i.e. if --skip_alignment false then all samples will go from STAR to Salmon quant. We could add a flag that is similar to --skip_alignment or --skip_pseudoalignment which prevents quantification, e.g. --skip_quantification, producing the relevant BAM files and any quality control but going no further.

The main use case would be people who wish to generate a BAM file with an RNA-aware alignment algorithm but are not performing a quantification experiment.

The other use case would be people who wish to use Salmon for read-mapping based quantification but also want to produce a BAM on the side:

flowchart TD
    A[Reads] -->|Filtering & QC| B(Filtered reads)
    B --> |STAR| C[BAM]
    B --> |SALMON| D[Counts]
    C --> |QC| F[Validation]
    D --> |Analysis| E[Interpretation]

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