From 89163ced41f416e8819dbee38872127fc114c58f Mon Sep 17 00:00:00 2001 From: Rike Date: Wed, 16 Aug 2023 17:19:22 +0200 Subject: [PATCH] remove view statement --- subworkflows/local/bam_joint_calling_germline_gatk/main.nf | 2 -- tests/test_joint_germline.yml | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf index 50c75b0c04..f0d9148c07 100644 --- a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf +++ b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf @@ -147,8 +147,6 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK { [[id:"joint_variant_calling", patient:"all_samples", variantcaller:"haplotypecaller"], tbi_out] } - genotype_vcf.view() - versions = versions.mix(GATK4_GENOMICSDBIMPORT.out.versions) versions = versions.mix(GATK4_GENOTYPEGVCFS.out.versions) versions = versions.mix(VARIANTRECALIBRATOR_SNP.out.versions) diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index ba19cf5aa2..6bd7b4532f 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -73,7 +73,7 @@ - vqsr files: - path: results/csv/variantcalled.csv - md5sum: 1a7e405250ac5f253197ebf4672b1f98 + md5sum: 8513cd4aef3f54e2a72940461617c6c7 - path: results/multiqc - path: results/preprocessing/recalibrated/test/test.recal.cram should_exist: false