Enable complex contrast strings in DESeq2

[delfiterradas]

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Closes nf-core/differentialabundance#515

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[pinin4fjords]

Thanks for this PR! The approach of using limma::makeContrasts() to parse complex contrast strings makes sense.

One thing I wanted to check - in the new limma branch, the shrinkage result is assigned to comp.shrunk:

comp.shrunk <- run_shrink(contrast = numeric_contrast)

But in the existing code path, it's assigned to comp.results:

comp.results <- run_shrink(coef = opt$contrast_string)

Is this intentional? I couldn't see comp.shrunk being used elsewhere, so I wondered if it should be comp.results for consistency - but I may be missing something.

Also noticed the test uses --shrink_lfc FALSE, so it might be worth adding a case with shrinkage enabled to cover that path.