# HG changeset patch
# User sanbi-uwc
# Date 1527600658 14400
# Node ID 395aac51afa6c61220e818dcf251a6a07eddfee1
# Parent  df170f4d2eeae93ea16e3ace61d5a8b5daabd3ab
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 1d2ba43f108038467c4b0b145ae3887e8f152f33

diff -r df170f4d2eea -r 395aac51afa6 novo_align.py
--- a/novo_align.py	Mon May 07 09:42:08 2018 -0400
+++ b/novo_align.py	Tue May 29 09:30:58 2018 -0400
@@ -10,7 +10,7 @@
 
 def novo_align(output_filename, index_filename, fwd_file, rev_file ):
     param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
-    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools sort - | samtools view -b - > {}".format(
+    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
         index_filename,
         fwd_file,
         rev_file,