diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3d8984c5..69b7f031 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -288,9 +288,9 @@ workflow RAREDISEASE { ch_target_intervals = ch_references.target_intervals ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [[id:it[0].simpleName],it]}.collect() : Channel.value([[],[]]) - ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).collect() + ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).collect() : Channel.value([]) - ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).collect() + ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).collect() : Channel.value([]) ch_vcfanno_resources = params.vcfanno_resources ? Channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() : Channel.value([])