# HG changeset patch
# User sanbi-uwc
# Date 1527674442 14400
# Node ID 8ed9bca5537030545e8019db32dc0523b8714ea6
# Parent  395aac51afa6c61220e818dcf251a6a07eddfee1
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit d7229ded9fe3ee86ce363a8fed29d5117c6c280e

diff -r 395aac51afa6 -r 8ed9bca55370 novo_align.py
--- a/novo_align.py	Tue May 29 09:30:58 2018 -0400
+++ b/novo_align.py	Wed May 30 06:00:42 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,