Mercurial > repos > sanbi-uwc > novo_sort
diff novo_sort.py @ 4:146641fe5ff6 draft
planemo upload for repository https://github.com/zipho/novo_sort commit 0bb684bfc6b3f1f07105117dfd71285ce4ff7f4e
author | sanbi-uwc |
---|---|
date | Fri, 01 Apr 2016 10:15:24 -0400 |
parents | 9c51aca51902 |
children | 6e11ef75c56c |
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--- a/novo_sort.py Fri Apr 01 09:53:18 2016 -0400 +++ b/novo_sort.py Fri Apr 01 10:15:24 2016 -0400 @@ -7,8 +7,8 @@ import logging log = logging.getLogger( __name__ ) -def novo_sort( bam_filename ): - cmdline_str = "novosort -c 8 -m 8G -s -f {}".format( bam_filename ) +def novo_sort( bam_filename, output_filename ): + cmdline_str = "novosort -c 8 -m 8G -s -f {} > {}".format( bam_filename, output_filename ) cmdline = newSplit(cmdline_str) try: check_call(cmdline) @@ -28,6 +28,6 @@ parser.add_argument('--bam_filename') args = parser.parse_args() - novo_sort(args.bam_filename) + novo_sort(args.bam_filename, output_filename) if __name__ == "__main__": main()