From 25b55df474acb70060551511809cb55fa9370f14 Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Tue, 29 Oct 2024 14:51:36 +0100 Subject: [PATCH] Remove genome from the subworkflow, too --- subworkflows/local/bam_variant_calling_somatic_purecn/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf b/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf index 4b5eb961a8..38921c591a 100644 --- a/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf @@ -16,7 +16,6 @@ workflow BAM_VARIANT_CALLING_SOMATIC_PURECN { fasta // channel: [mandatory] fasta needed for cram fasta_fai // channel: [mandatory] fasta index needed by GATK dict // channel: [mandatory] fasta dictionary needed by GATK - genome // channel: [mandatory] genome used for interval parsing normaldb // channel: [mandatory] panel of normals built by PureCN gatk_pon // channel: [mandatory] panel of normals used by GATK for denoising intervals_bed // channel: [mandatory] BED file processed by PureCN @@ -47,7 +46,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_PURECN { } //FIXME: PURECN_RUN upstream should require a VCF file here - PURECN_RUN(ch_purecn_in, normaldb, genome) + PURECN_RUN(ch_purecn_in, normaldb) ch_versions = ch_versions.mix(PURECN_RUN.out.versions) emit: