Plastid

[suhrig]

This PR incorporates the new plastid module into the pipeline. This is the first step to making quantification of Ribo-seq data more accurate. It enables us to quantify Ribo-seq reads which are in-frame instead of counting the raw reads.

The second step will be to incorporate the counts into the downstream analyses. I will wait with this until the current improvements around the quantification scripts have been completed (@pinin4fjords is currently working on this AFAIK).

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[suhrig]

@nf-core-bot fix linting

[pinin4fjords]

Nice, but the workflow logic in particular can be simplified