Addition of --mergeContext for MethylDackel

[dcarrillox]

Description of feature

Hi,

Have you considered adding the --mergeContext option for the bwameth + MethylDackel workflow? It collapses methylation calls at Cytosine level to CpG site level, and the same goes for the CHG and CHH contexts if --comprehensive is used.

I think it could be a very interesting addition which also would simplify downstream analysis.

Thanks,
Daniel

[sateeshperi]

hi @dcarrillox sounds like a good idea! Do you have any docs reference for the --mergeContext option ?

[dcarrillox]

Hi @sateeshperi, yes! This feature is explained in the Per-CpG/CHG metrics section of the MethylDackel README

[sateeshperi]

the bwameth subworkflow would soon be available as standalone in nf=core/modules repo.
PR here

Would you be interested in contributing to this feature ?

[dcarrillox]

Hi @sateeshperi, yes I can try. Any particular aspect you think I could start with?

[sateeshperi]

hi @dcarrillox could you take a look at the branch that is linked to this issue and if you could verify that the bed graphs now indeed produce merged contexts when running with comprehensive ? that would be gr8