# HG changeset patch
# User trinity_ctat
# Date 1523645968 14400
# Node ID 3268b5e6ab4a6a959bdb70ac1f6164689c54a84a
# Parent  dc3454ad7e09609a4f4e0e34a2318c0f276eb24b
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.

diff -r dc3454ad7e09 -r 3268b5e6ab4a ctat_star_fusion.xml
--- a/ctat_star_fusion.xml	Thu Apr 12 14:19:02 2018 -0400
+++ b/ctat_star_fusion.xml	Fri Apr 13 14:59:28 2018 -0400
@@ -8,8 +8,8 @@
         are not in it at the current time.
         -->
 	<requirement type="package">perl-carp</requirement>
-	<requirement type="package">perl-json-xs<plrequirement>
-	<requirement type="package">perl-io-gzip<plrequirement>
+	<requirement type="package">perl-json-xs</requirement>
+	<requirement type="package">perl-io-gzip</requirement>
         <requirement type="package">samtools</requirement>
         <!--
         FIX - If samtools is really a requirement, shouldn't it be a star-fusion dependency?
@@ -18,6 +18,15 @@
         <requirement type="package" version="1.3">samtools</requirement>
         -->
     </requirements>
+    <!-- Using command's detect_errors instead of below.
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
+    </stdio>
+    <regex match="Must investigate error above."
+           source="stderr"
+           level="fatal"
+           description="Unknown error encountered" />
+    -->
     <command detect_errors="default">
       <![CDATA[
       STAR-Fusion
@@ -27,13 +36,6 @@
         --output_dir subdir
       ]]>
     </command>
-    <stdio>
-      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
-    </stdio>
-    <regex match="Must investigate error above."
-           source="stderr"
-           level="fatal"
-           description="Unknown error encountered" />
 
     <inputs>
       <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>