in-frame p-site quantification method

[suhrig]

This PR adds another (experimental) quantification method for Ribo-seq data. Instead of counting all Ribo-seq reads which map to a transcript, this new method only counts reads which map to coding regions (CDS) and only if the P-sites computed by Plastid align with the reading frame of the coding region. This means the quantification method is fairly conservative, ignoring frame-shifted reads or reads mapping to unannotated coding regions. RNA-seq quantification is unchanged.

The user can enable this quantification method by setting --te_quantification_method to the value plastid_psite. It is off by default. The method is implemented as a local module (essentially bedtools intersect).

I meant to add a test for this new quantification method, but the inputs to the module are not deterministic to begin with which means the outputs aren't either, making a test rather pointless.

PR checklist

• This comment contains a description of changes (with reason).
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[suhrig]

@nf-core-bot fix linting