Deseq2 spike handling

[pinin4fjords]

This PR adds the ability to generate size factors in DESeq2 using a limited set of control genes, as is sometimes performed with technical controls such as ERCC spike-ins.

Based on https://support.bioconductor.org/p/9143354/ and the DESeq2 docs.

Note that if spikes are present, but the spike handling option is not selected, then the spikes are stripped so they do not participate in normalisation (since they could generate artefacts if left in place).

PR checklist

Closes #2440

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[edmundmiller]

Code looks great to me! I'm wondering if controlling it with the nextflow config is going to be more hassle, or if that should live in the script directive and be configured based on the input params. Instead, right now the end user has to figure out how to use it.

[pinin4fjords]

Code looks great to me! I'm wondering if controlling it with the nextflow config is going to be more hassle, or if that should live in the script directive and be configured based on the input params. Instead, right now the end user has to figure out how to use it.

@emiller88 Could you expand on that a bit? It can't be automatically configured based on whether or not spikes are applied, because there are two modes:

1. Supply the spikes, but just so we can strip them from the matrix so they don't bias the global normalisation
2. Supply the spikes, so they can be used to generate scaling factors

... which is what --sizefactors_from_controls in the nextflow.config differentiates. How would you like to see that change?

Edit: I've added info on --sizefactors_from_controls to the meta.yaml. That's a bit non-standard, but I think justified given that this is a parameter I devised for the wrapper, rather than something native to DESeq2.

[pinin4fjords]

@emiller88 I'm going to go ahead and merge this with the two approvals. Happy to make adjustments in future PRs if you get time to expand on your suggestion at some point.