# HG changeset patch # User jackcurragh # Date 1652364948 0 # Node ID ca7c965f7cc99b903ee267540203aa3b0423edd3 # Parent b49ad9f12dfa1c9517ea9740fd9d51d7f6953361 Uploaded diff -r b49ad9f12dfa -r ca7c965f7cc9 bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py --- 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 ) diff -r b49ad9f12dfa -r ca7c965f7cc9 bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml --- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml Wed May 11 13:37:35 2022 +0000 +++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml Thu May 12 14:15:48 2022 +0000 @@ -1,7 +1,7 @@ - bowtie + bowtie bowtie --version @@ -420,7 +420,7 @@ - + diff -r b49ad9f12dfa -r ca7c965f7cc9 bowtie_rRNA_removal_wrapper/test-data/output.bam Binary file bowtie_rRNA_removal_wrapper/test-data/output.bam has changed diff -r b49ad9f12dfa -r ca7c965f7cc9 bowtie_rRNA_removal_wrapper/test-data/output.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_rRNA_removal_wrapper/test-data/output.sam Thu May 12 14:15:48 2022 +0000 @@ -0,0 +1,10003 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:9 LN:5999940 +@PG ID:Bowtie VN:1.2.3 CL:"/usr/bin/bowtie-align-s --wrapper basic-0 -v 3 -S -p 6 test -q test.fastq" +NS500289:1032:HMFHFBGXK:2:11101:14792:13153 4 * 0 0 * * 0 0 CCGCCGAGGGCGCACCACCGGCCCGTCTCAC AAEEEEEEEEEEEEEEEEEEEEEEEEEEE6E XM:i:0 +NS500289:1032:HMFHFBGXK:2:11101:21043:15993 4 * 0 0 * * 0 0 CCCCCGCGGGGGCGCGCCGGCGTGGGGGGGCCGGGGC AAEEEEEAAAEEEEEE/AEE/EEEEE6E66/A/A//E XM:i:0 +NS500289:1032:HMFHFBGXK:2:11101:20421:20097 4 * 0 0 * * 0 0 CTGTCCACCTTCCAGCAGATGTGGATCAGC AA/EAEEEEEEEEE6E