# HG changeset patch
# User sanbi-uwc
# Date 1525700528 14400
# Node ID df170f4d2eeae93ea16e3ace61d5a8b5daabd3ab
# Parent  709eb84d9927f57d633cb055508ab25acc7726eb
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 018e4e2f405e9e55f3b7c3ba92b29f957e468f2b

diff -r 709eb84d9927 -r df170f4d2eea novo_align.py
--- a/novo_align.py	Mon May 07 06:44:07 2018 -0400
+++ b/novo_align.py	Mon May 07 09:42:08 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 view -bS - > {}".format(
+    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools sort - | samtools view -b - > {}".format(
         index_filename,
         fwd_file,
         rev_file,