Description of the bug

Hi Developers,

I'm trying to run the Sarek implemented ASCAT for CNV analysis on WES data. On the nfcore Sarek website, it's suggested to follow 5 steps, as specified in this doc https://nf-co.re/sarek/3.4.0/docs/usage#how-to-generate-ascat-resources-for-exome-or-targeted-sequencing, to generate reference information (allele.zip, loci.zip, GC.zip, and RT.zip) for exome data instead of using the default igenome directly. I noticed that the ASCAT author had also provided ref files for WES at https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES, which seemed to be a ready-to-use version when provided with an appropriate BED file. Would it be feasible to replace the default ignome ref with those for Sarek ASCAT?

I'm now running Sarek with params (-- --ascat_alleles, --ascat_loci, --ascat_loci_gc, --ascat_loci_rt) on the command line. The pipeline seems to work well. But, it would be great to hear advice from you.

Thank you!

Command used and terminal output

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Relevant files

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System information

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