Salmon quant with UMI-tools does not work

[grst]

Running the pipeline with umi-tools and salmon quantification results in wrong counts.

There are two issues:

• umi-tools is ran without the --paired flag with paired end data (TODO: fix module)
• umi-tools does not include unmapped mates, while Salmon expects them to be present

See also discussion at CGATOxford/UMI-tools#465) and COMBINE-lab/salmon#684.

[drpatelh]

Module updated here nf-core/modules#583

[drpatelh]

Pipeline updated here #669

[grst]

This solved the issue 🎉

The results of the DE are now very, very similar to the feature counts version I used before.
I think this is good enough for now! If Ian comes up with some magic to handle unpaired reads in UMI-tools we can still incorporate that later.