Jonathan Manning

Thanks @SPPearce - appreciate the info, the rationale is clearer to me now, and it makes sense not to have the global parameters. Will update the PR notes to match...

> does it error if you provide an unexpected argument (i.e. a typo)? Yep! https://github.com/nf-core/modules/blob/d59f148cb848b4afabc6d6c2041651f28610bddb/modules/nf-core/deseq2/differential/templates/deseq_de.r#L67 > Are you expecting the contrast_meta to be constructed from rows of a csv file?...

> Does this shrink the log2FC values automatically? I can't see it. I'm pretty sure it happens in `DESeq2()` for calculating the p values etc, but I haven't applied it...

> > > Does this shrink the log2FC values automatically? I can't see it. > > > I'm pretty sure it happens in `DESeq2()` for calculating the p values etc,...

> Does this shrink the log2FC values automatically? I can't see it. I'm going to revise my earlier response with this from the DESeq docs: _"An option in DESeq2 is...

(note: singularity failure is just because we're waiting for a build to propagate from biocontainers)

Thanks @ggabernet! I'm just going to switch the inputs to be keyed by the meta- as per feedback in https://github.com/nf-core/modules/pull/2321, will do that quickly now.

> One thing that could be done to also test the blocking variables and that the execution with multiple contrasts works fine would be to add another contrast in the...

Thanks @ggabernet (and apologies I just saw this). I was confused in the other review - it seemed like the meta thing was pretty non-negotiable (though as it turned out...

Thanks for the review @ggabernet !