I think there are two issues here and we can divide this in two tickets:

1. When running the pipeline with DREAM, VARIANCEPARTITION_DREAM is only executed once, even though there are three contrasts. This is the reason of the issue:
   

   differentialabundance/subworkflows/nf-core/abundance_differential_filter/main.nf

   Lines 152 to 156 in dab78ce

   	// DREAM only runs with formula
   	dream_inputs = inputs.contrasts_for_diff_with_formula
   	.filter { meta, _variable, _reference, _target, formula, _comparison ->
   	meta.differential_method == 'dream' && formula != null
   	}

Do we want to process non-formula constrasts with DREAM as well?

Originally posted by @atrigila in #533