Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py @ 5:b300c15426f5 draft

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author jackcurragh
date Mon, 21 Mar 2022 12:53:51 +0000
parents 9424721e6296
children 82854aad329b
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line diff
--- 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: