From b05565706b7ce076894d498091c50316713c9194 Mon Sep 17 00:00:00 2001
From: bshifaw <bshifaw@broadinstitute.com>
Date: Thu, 4 Feb 2021 17:12:27 -0500
Subject: [PATCH] add set e to gtfToCallingIntervals (#6)

---
 gatk4-rna-best-practices.wdl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gatk4-rna-best-practices.wdl b/gatk4-rna-best-practices.wdl
index d70df28..217f17f 100644
--- a/gatk4-rna-best-practices.wdl
+++ b/gatk4-rna-best-practices.wdl
@@ -256,6 +256,9 @@ task gtfToCallingIntervals {
     Int preemptible_count
 
     command <<<
+
+	set -e
+
         Rscript --no-save -<<'RCODE'
             gtf = read.table("${gtf}", sep="\t")
             gtf = subset(gtf, V3 == "exon")