Removing old annotation code

[arvados-tutorial.git] / cwl / bwa-gatk-wf.cwl

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
index 675bdd04d86f6568c5855278bed45c0b79f928fa..6e1f326127baf9e2e016bfd2bad1c3c7d0b838ce 100644 (file)
--- a/cwl/bwa-gatk-wf.cwl
+++ b/cwl/bwa-gatk-wf.cwl
@@ -60,9 +60,3 @@ steps:
       bam: samtools-index/out
       sample: sample
     out: [vcf]
-  vep:
-    run: vep.cwl
-    in:
-      vcf: haplotypecaller/vcf
-      sample: sample
-    out: [out-vcf]