CADD for chr? chromosome names

[fa2k]

Description of the bug

CADD doesn't work for references with chr1, chr2, ...

No CADD score is added to indels.

The nallo pipeline has fixed it and I'm thinking of porting over this fix - https://github.com/genomic-medicine-sweden/nallo/blob/dev/subworkflows/local/annotate_cadd/main.nf

It will make CADD slightly slower for references that already have compatible chromosome names.

Command used and terminal output

Relevant files

No response

System information

No response

[fellen31]

Nice catch! If you port it, perhaps you could add the subworkflow to nf-core instead? Then we can install it from there and use the exact same for Nallo and raredisease. Started the process with another subworkflow (nf-core/modules#8777) and some modules.

[fa2k]

That's a fair point, I'll have a look at how to make it a subworkflow. Already have a prototype for changes to raredisease that I'm testing now https://github.com/fa2k/raredisease/tree/cadd-chrnames