# HG changeset patch
# User iuc
# Date 1523400010 14400
# Node ID 6def3ba376a738becf79171e4262cc8e6574fe0c
# Parent  29299da15326b991456502ad452fd550a8c1b67f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c

diff -r 29299da15326 -r 6def3ba376a7 bwa-mem.xml
--- a/bwa-mem.xml	Thu Feb 01 12:35:18 2018 -0500
+++ b/bwa-mem.xml	Tue Apr 10 18:40:10 2018 -0400
@@ -8,6 +8,7 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
+@pipefail@
 @set_reference_fasta_filename@
 
 ## Begin BWA-MEM command line
diff -r 29299da15326 -r 6def3ba376a7 bwa.xml
--- a/bwa.xml	Thu Feb 01 12:35:18 2018 -0500
+++ b/bwa.xml	Tue Apr 10 18:40:10 2018 -0400
@@ -78,6 +78,7 @@
     <expand macro="stdio"/>
     <command>
         <![CDATA[
+@pipefail@
 @set_reference_fasta_filename@
 
 ## setup vars for rg handling...
diff -r 29299da15326 -r 6def3ba376a7 bwa_macros.xml
--- a/bwa_macros.xml	Thu Feb 01 12:35:18 2018 -0500
+++ b/bwa_macros.xml	Tue Apr 10 18:40:10 2018 -0400
@@ -3,6 +3,8 @@
 
     <token name="@VERSION@">0.7.17</token>
 
+    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
+
     <token name="@set_rg_string@">
         #set $rg_string = "@RG\\tID:" + str($rg_id)
         #set $rg_string += $format_read_group("\\tSM:", $rg_sm)