Mercurial > repos > sanbi-uwc > novo_align
changeset 30:49ff46f3cd17 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 4f9ecd34b5509fb702812786f5a3db6393f9fa25
author | sanbi-uwc |
---|---|
date | Wed, 30 May 2018 07:25:37 -0400 |
parents | 8ed9bca55370 |
children | 4d92ef6639a2 |
files | novo_align.py |
diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/novo_align.py Wed May 30 06:00:42 2018 -0400 +++ b/novo_align.py Wed May 30 07:25:37 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,