From 01aa41d21addca2002f1269ba41e165c33e9e03e Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 30 Jun 2022 14:09:40 +0200
Subject: [PATCH] fix heredoc

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

diff --git a/gridss.wdl b/gridss.wdl
index 0070539..0e8fd43 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -94,7 +94,7 @@ task AnnotateSvTypes {
     command <<<
         set -e
         mkdir -p "$(dirname ~{outputPath})"
-        R --vanilla << EOF
+        R --vanilla << "EOF"
         library(VariantAnnotation)
         library(StructuralVariantAnnotation)
 
@@ -115,7 +115,7 @@ task AnnotateSvTypes {
         gr <- breakpointRanges(vcf)
         svtype <- simpleEventType(gr)
         info(vcf[gr$sourceId])$SVTYPE <- svtype
-        writeVcf(vcf, out_path)
+        writeVcf(vcf, out_path, index=T)
         EOF
     >>>
 
-- 
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