Add dream module

[nschcolnicov]

PR checklist

Closes https://github.com/nf-core/differentialabundance/issues/363

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[atrigila]

Nico, I found several issues and errors in this original module. I've been re-writing a little bit differently. I am going to push my changes and suggestions here + the migration to the template form.

[atrigila]

@nschcolnicov feel free to check if these changes suit the pipeline structure and what you and Alan envisioned and if all looks good to you we could ask for reviewers.

[atrigila]

Ping @grst for final review

[atrigila]

The errors seem to be unrelated to this module:

• The linting failing is in differential_functional_enrichment. It seems like empty md5sums are now detected. I did not change the snapshot or the files here. These empty files seem to previously be in the snapshot.
• The tests failing are also unrelated to the changes in this module. For example, it looks like this file "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv and this file treatment_mCherry_hND6__test_limma_voom.limma.results.tsv have different md5sums. These failing tests seem to be the same as here: https://github.com/nf-core/modules/pull/7870, where there was a very simple, minimal change in the tag (should not affect any result). It seems like tests related to limma seem to fail?

[pinin4fjords]

Guys, I have a huge problem with the dream treatment in the differential subworkflow here.

The idea of that subworkflow is that differential methodology is dictated by channel content. There shouldn't be a custom input channel for dream, or a custom output channel, or the calling workflow will have to do different things for the dream case, which is very bad.

Side note: could you please make sure you seek review from a listed maintainer when PR'ing?

[grst]

Agree that dream shouldn't have separate channels. Sorry, I didn't pay close attention to the subworkflow, I was more looking at R script.

Also worth mentioning that we see dream as a test run for providing the model specification as a formula (because you can't easily specify a mixed effect with blocking factors), so it's worth making sure this part also matches your expectations, @pinin4fjords