if reference is provided then no bed file

FriederikeHanssen · FriederikeHanssen · commit fb1e756a5561 · 2022-07-17T16:51:27.000+02:00
diff --git a/subworkflows/local/tumor_variant_calling.nf b/subworkflows/local/tumor_variant_calling.nf
@@ -103,7 +103,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
         RUN_CNVKIT ( cram_recalibrated_cnvkit_tumoronly,
                         fasta,
                         fasta_fai,
-                        intervals_bed_combined,
+                        [],
                         cnvkit_reference )
 
         ch_versions = ch_versions.mix(RUN_CNVKIT.out.versions)
