Pair file documentation missing from DNAseq somatic docs

[MareikeJaniak]

Hi Shaloo,

A user brought an oversight in the documentation for the new merged DNAseq protocol to our attention. In the old documentation for the TumorPair pipeline, we documented the option for the -p PAIRS_FILE that's needed for the paired somatic protocols. This is missing in the new merged documentation for the DNASeq pipeline.

Could you incorporate the information on the pairs file that's here: https://genpipes.readthedocs.io/en/genpipes-v4.6.1/user_guide/pipelines/gp_tumourpair.html into the current documentation for DNASeq? There is reference to it under "Options" and there is a box with more info at the bottom of the page.

The -p option is mandatory for running the protocols somatic_fastpass, somatic_ensemble, and somatic_sv.

Best,
Mareike