Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 27:7b142d90bb06 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Tue, 12 Jul 2022 13:22:56 +0000 |
| parents | ca7c965f7cc9 |
| children | 44e61af3637d |
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--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py Fri May 27 10:28:39 2022 +0000 +++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py Tue Jul 12 13:22:56 2022 +0000 @@ -392,7 +392,19 @@ keepends = '--col-keepends' else: keepends = '' - aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ + if options.output_unmapped_reads_l or options.output_unmapped_reads_r or options.output_unmapped_reads: + aligning_cmds = '-q %s %s -p %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ + '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ + ( maxInsert, mateOrient, options.threads, suppressHeader, + colorspace, skip, alignLimit, trimH, trimL, maxMismatches, + mismatchSeed, mismatchQual, seedLen, rounding, minInsert, + maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, + tryHard, valAlign, allValAligns, suppressAlign, best, + strata, offrate, seed, snpphred, snpfrac, keepends, + output_unmapped_reads, output_suppressed_reads, + quality_score_encoding ) + else: + aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, skip, alignLimit, trimH, trimL, maxMismatches,