Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 22:ca7c965f7cc9 draft

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Uploaded
author jackcurragh
date Thu, 12 May 2022 14:15:48 +0000
parents b49ad9f12dfa
children 7b142d90bb06
line wrap: on
line diff
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Wed May 11 13:37:35 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Thu May 12 14:15:48 2022 +0000
@@ -414,9 +414,13 @@
             if options.output != 'XXXX':
                 print('incorrect option')
                 if options.paired == 'paired':
-                    cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
+                    # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
+                    cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+
                 else:
-                    cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
+                    # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
+                    cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+
             else:
                 if options.paired == 'paired':
                     cmd2 = 'bowtie %s %s -1 %s -2 %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2 )