# HG changeset patch
# User sanbi-uwc
# Date 1527712256 14400
# Node ID 4d92ef6639a265a4cc49fdf4e607d0d75b523b1d
# Parent  49ff46f3cd17882ad7d6cceafa217778f3e2c4bc
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 4599a515144aa8f69b28cdad006eed61bbe94b53

diff -r 49ff46f3cd17 -r 4d92ef6639a2 novo_align.py
--- a/novo_align.py	Wed May 30 07:25:37 2018 -0400
+++ b/novo_align.py	Wed May 30 16:30:56 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 view -bS - > {}".format(
         index_filename,
         fwd_file,
         rev_file,