Diana Kolbe
04/28/2026, 6:54 PMAnalysis options
analysis_type : wes
skip_subworkflows : mt_annotation,mt_subsample,me_calling,me_annotation,repeat_annotation,repeat_calling,snv_annotation,snv_calling,sv_annotation,generate_clinical_set
skip_tools : fastp,gens,haplogrep3,peddy,smncopynumbercaller,vcf2cytosure,fastqc,qualimap,eklipse,ngsbits
I'm getting a parameter validation error:
* Missing required parameter(s): intervals_wgs, intervals_y
Previous discussion on these params indicate they're for WGS coverage stats and not appropriate for WES, and it seems like this was addressed - https://github.com/nf-core/raredisease/pull/396#event-10006745584
Any way to skip this or get this validation to be quiet, or just pull/generate the files in order to provide them?