1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f9da9ca5ccae/ changeset: f9da9ca5ccae user: dan date: 2012-01-25 18:11:27 summary: Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq. affected #: 1 file
diff -r fd6f22c072f3b2acbde3311943af004f1094a4fa -r f9da9ca5ccae7ead780d0331102cda204e38d646 tools/picard/picard_SamToFastq_wrapper.py --- a/tools/picard/picard_SamToFastq_wrapper.py +++ b/tools/picard/picard_SamToFastq_wrapper.py @@ -80,13 +80,13 @@ shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name ) fastq_1_name = None else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastq' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) + shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) elif filename.endswith( '_2.fastq' ): if fastq_2_name: shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name ) fastq_2_name = None else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastq' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) ) + shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) )
cleanup_before_exit( tmp_dir )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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