Allow flexibility in meta map usage with Deseq2

[pinin4fjords]

PR checklist

This PR establishes some consistency with feedback from @jfy133 in another PR. Essentially we should not be 'baking in' assumptions about the content meta maps, but rather allowing the workflow-level usage to pass that.

So, where the R template was previously reading the meta directly, it now receives the meta options like by setting the following in the workflow configs:

ext.args = { "--contrast_variable $meta.variable --reference_level $meta.reference --treatment_level $meta.target --blocking_variables $meta.blocking "}

I've also tweaked the bare-bones option parsing there to allow for blank values passed that way.

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[WackerO]

Other than those two comments, LGTM!

[pinin4fjords]

Thanks for the review @WackerO