Can I force run without --bed option?

[AhmedArslan]

I want to analyse all the regions of genome.

[PhilPalmer]

Hi @AhmedArslan really sorry for the late reply,

Unfortunately bed is a required argument so the pipeline will fail if it is not specified

If you want to force it to run you could try deleting this line and if I'm not mistaken that should work for a whole genome analysis. You will then specify a dummy file for bed parameter eg an empty text file would work 😅

Feel free to let me know if that works. I'll also tag this as a feature request to make the bed parameter optional as a proper solution going forward