Description of feature

Currently, the pipeline considers as a biological replicate any sample which has the same id under the sample column of the samplesheet followed by a different suffix determined by an underscore e.g.:

sample1_r1
sample1_r2
sample2_r1
sample2_r2

This information is used by the pipeline in this code line to determine whether multiple groups are present e,g, sample1 and sample2 in the example above and whether replicates exists r1 and r2 also using the example above.

However, the problem with this approach is that is based on the sample names and sometimes this can be problematic since depends on the correct naming of the replicates with the underscore, see this issue.

I guess that the solution to this problem will be to include again the replicate column into the samplesheet, although this information is currently only used for enabling the run of DESEQ2_QC here and MACS2_CONSENSUS here.

I would like to know your opinion here @drpatelh, @bjlang and any other willing to give feedback of course :smi