Mercurial > repos > sanbi-uwc > novo_align

changeset 29:8ed9bca55370 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit d7229ded9fe3ee86ce363a8fed29d5117c6c280e
author sanbi-uwc
date Wed, 30 May 2018 06:00:42 -0400
parents 395aac51afa6
children 49ff46f3cd17
files novo_align.py
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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,