The nf-core/rnaseq pipeline has support for this via giving the same sample name to indicate technical replicates. It"s particularly important for Salmon counts, where post-pipeline merging of replicates at the counts matrix level is not a good way to handle it.

The older RNAsik pipeline UI supports this by guessing sample names, but allowing the user to change them (eg, so technical reps could be manually renamed to the same sample name). We should add this feature to the nf-core/rnaseq setup form.

Related: #217 and #85