Mercurial > repos > sanbi-uwc > novo_sort

diff novo_sort.py @ 6:e35fbd921b6b draft

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planemo upload for repository https://github.com/zipho/novo_sort commit 7cef20d7d397e9e8e1c64872c2f31417f31ed964
author sanbi-uwc
date Fri, 01 Apr 2016 10:26:19 -0400
parents 6e11ef75c56c
children 2f3d4c867e1d
line wrap: on
line diff
--- a/novo_sort.py	Fri Apr 01 10:16:18 2016 -0400
+++ b/novo_sort.py	Fri Apr 01 10:26:19 2016 -0400
@@ -8,7 +8,7 @@
 log = logging.getLogger( __name__ )
 
 def novo_sort( bam_filename, output_filename ):
-    cmdline_str = "novosort -c 8 -m 8G -s -f {} > {}".format( bam_filename, output_filename )
+    cmdline_str = "novosort -c 8 -m 8G -s -f {} -o {}".format( bam_filename, output_filename )
     cmdline = newSplit(cmdline_str)
     try:
         check_call(cmdline)