From bcfb73e3d855bf01173474fead84f6428c79393f Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 8 Sep 2022 15:20:24 +0200 Subject: [PATCH] harmonize syntax --- .../nf-core/gatk4/joint_germline_variant_calling/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf b/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf index 4beab66c3a..c2427c05b4 100644 --- a/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf @@ -64,9 +64,9 @@ workflow GATK_JOINT_GERMLINE_VARIANT_CALLING { //Sort vcfs called by interval within each VCF // - vcfs = GATK4_GENOTYPEGVCFS ( genotype_input, fasta, fai, dict, dbsnp, dbsnp_tbi).vcf + GATK4_GENOTYPEGVCFS (genotype_input, fasta, fai, dict, dbsnp, dbsnp_tbi) - BCFTOOLS_SORT(vcfs) + BCFTOOLS_SORT(GATK4_GENOTYPEGVCFS.out.vcf) vcfs_sorted_input = BCFTOOLS_SORT.out.vcf.branch{ intervals: it[0].num_intervals > 1 no_intervals: it[0].num_intervals <= 1