remove view statement

nf-core · Aug 16, 2023 · 89163ce · 89163ce
1 parent 4aab558
commit 89163ce
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diff --git 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
@@ -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