From db670884d277ab4acacebc3d33cc9cd0111df625 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 17 Mar 2023 10:10:04 +0100
Subject: [PATCH] fix wdl syntax error

---
 WGSinCancerDiagnostics.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/WGSinCancerDiagnostics.wdl b/WGSinCancerDiagnostics.wdl
index ccc01b8..e7794d2 100644
--- a/WGSinCancerDiagnostics.wdl
+++ b/WGSinCancerDiagnostics.wdl
@@ -929,14 +929,14 @@ task MakeVafTable {
         String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
     }
 
-    command {
+    command <<<
         set -eo pipefail
         bcftools query \
         -i 'FILTER="PASS"' \
         -f '%CHROM\t%POS\t%INFO/PURPLE_AF\n' \
         ~{purpleSomaticVcf} | \
         { grep -v '^MT' > ~{outputPath} || true; }
-    }
+    >>>
 
     output {
         File vafTable = outputPath