Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py @ 5:b300c15426f5 draft
Uploaded
author | jackcurragh |
---|---|
date | Mon, 21 Mar 2022 12:53:51 +0000 |
parents | 9424721e6296 |
children | 82854aad329b |
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--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py Tue Mar 15 10:27:46 2022 +0000 +++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py Mon Mar 21 12:53:51 2022 +0000 @@ -414,7 +414,7 @@ if options.paired == 'paired': cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) else: - cmd2 = 'echo "bowtie %s %s %s > %s" > ~/galaxy_test.txt' % ( aligning_cmds, ref_file_name, options.input1, options.output ) + cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) # align tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name with open(tmp, 'w') as tmp_stderr: