# HG changeset patch
# User sanbi-uwc
# Date 1459520124 14400
# Node ID 146641fe5ff6a2fae4c0ae297555a5308ce29eea
# Parent  9c51aca51902b14fa4ef44721492089f652c9e78
planemo upload for repository https://github.com/zipho/novo_sort commit 0bb684bfc6b3f1f07105117dfd71285ce4ff7f4e

diff -r 9c51aca51902 -r 146641fe5ff6 novo_sort.py
--- a/novo_sort.py	Fri Apr 01 09:53:18 2016 -0400
+++ b/novo_sort.py	Fri Apr 01 10:15:24 2016 -0400
@@ -7,8 +7,8 @@
 import logging
 log = logging.getLogger( __name__ )
 
-def novo_sort( bam_filename ):
-    cmdline_str = "novosort -c 8 -m 8G -s -f {}".format( bam_filename )
+def novo_sort( bam_filename, output_filename ):
+    cmdline_str = "novosort -c 8 -m 8G -s -f {} > {}".format( bam_filename, output_filename )
     cmdline = newSplit(cmdline_str)
     try:
         check_call(cmdline)
@@ -28,6 +28,6 @@
     parser.add_argument('--bam_filename')
     args = parser.parse_args()
    
-    novo_sort(args.bam_filename)
+    novo_sort(args.bam_filename, output_filename)
 
 if __name__ == "__main__": main()