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diff flexbar_split_RR_bcs.xml @ 58:bbbae1ee87e0 draft default tip

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fix for flexbar with small data issue
author rnateam
date Tue, 16 Feb 2016 10:08:58 -0500
parents 25ebec14969a
children
line wrap: on
line diff
--- a/flexbar_split_RR_bcs.xml	Mon Feb 15 07:32:50 2016 -0500
+++ b/flexbar_split_RR_bcs.xml	Tue Feb 16 10:08:58 2016 -0500
@@ -14,7 +14,7 @@
 
     <version_command>flexbar --version</version_command>
 
-    <command>
+    <command><![CDATA[
 
         flexbar
 
@@ -49,14 +49,16 @@
         --max-uncalled $maxUncalled
         --min-read-length $minReadLen
 
-        > $output;
+        > $output
 
-        mv flexbar_barcode_repA_1.fastq $output_repA_1;
-        mv flexbar_barcode_repA_2.fastq $output_repA_2;
-        mv flexbar_barcode_repB_1.fastq $output_repB_1;
-        mv flexbar_barcode_repB_2.fastq $output_repB_2;
+        && mv flexbar_barcode_repA_1.fastq $output_repA_1
+        && mv flexbar_barcode_repA_2.fastq $output_repA_2
+        && mv flexbar_barcode_repB_1.fastq $output_repB_1
+        && mv flexbar_barcode_repB_2.fastq $output_repB_2
 
-    </command>
+        && sleep 20
+
+    ]]></command>
 
 
     <inputs>