Request to include M1UK typing to LinuxWADE.R

[PierreLyons]

Would it be possible to include the EMM_V_pipeline function call to the LinuxWADE.R script to allow M1UK typing?

The only issue I've seen with adding this function call to LinuxWADE.R is that EMM_V_pipeline will use file.choose() to get the user to select the snvTable.tsv output from SNPhyl, and this won't work in the command line. I've hard coded my local EMM_V_pipeline with the filepath to snvTable.tsv and it works in my case, but this would then break the functionality of the EMM_V_pipeline when running in Windows.

Thanks.