"--skip_umitools_extract" feature

[m3hdad]

Description of feature

In some cases the UMIs are provided as a third file. To get the files ready for the current version we have to add the UMIs to one of the fastQ files first and then proceed --with_umi option.

As discussed on slack#rnaseq, adding the third file breaks samplesheet format and the downstream channels/logic.

It would be simple and straightforward to handle this scenario outside the pipeline to get UMIs in both the read files and simply skip umi_tools extract but still traverse through the umi_tools dedup path.

[drpatelh]

Fixed in #807