From d38c467429a0637109a452ac63215f988eda9b36 Mon Sep 17 00:00:00 2001
From: Danny Park <dpark@broadinstitute.org>
Date: Fri, 10 Sep 2021 17:32:45 -0400
Subject: [PATCH] update vadr alert output column due to change in output
 format

---
 pipes/WDL/tasks/tasks_ncbi.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
index cccee4e37..248b16276 100644
--- a/pipes/WDL/tasks/tasks_ncbi.wdl
+++ b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -936,7 +936,7 @@ task vadr {
     tar -C "~{out_base}" -czvf "~{out_base}.vadr.tar.gz" .
 
     # prep alerts into a tsv file for parsing
-    cat "~{out_base}/~{out_base}.vadr.alt.list" | cut -f 2 | tail -n +2 \
+    cat "~{out_base}/~{out_base}.vadr.alt.list" | cut -f 5 | tail -n +2 \
       > "~{out_base}.vadr.alerts.tsv"
     cat "~{out_base}.vadr.alerts.tsv" | wc -l > NUM_ALERTS
   >>>