From b11c6ebcf2300a51ed9c2b3f9eee76d6a0163f39 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 27 Feb 2020 18:54:54 +0000
Subject: [PATCH] Removing old annotation code Arvados-DCO-1.1-Signed-off-by:
 Sarah Wait Zaranek <swz@curii.com> no issue #

---
 cwl/bwa-gatk-wf.cwl | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
index 675bdd0..6e1f326 100644
--- 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]
-- 
2.30.2