Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / scripts / htsw-runfolder

diff --git a/scripts/htsw-runfolder b/scripts/htsw-runfolder
index 53bceeff47e920b5e9ddf2696272f7a17d2ec139..e0b993776e7f52d4f0d0ebc9aa1a7f5feceb2dbe 100755 (executable)
--- a/scripts/htsw-runfolder
+++ b/scripts/htsw-runfolder
@@ -174,9 +174,9 @@ def make_parser():
                       help='create srf files tagged with the provided '\
                       'site name')
     parser.add_option('--raw-format', dest="raw_format", default='qseq',
-                      choices=['qseq', 'srf'],
+                      choices=['qseq', 'srf', 'fastq'],
                       help='Specify which type of raw format to use. '
-                           'Currently supported options: qseq, srf')
+                           'Currently supported options: qseq, srf, fastq')
     parser.add_option('-u', '--use-run', dest='use_run', default=None,
                       help='Specify which run to use instead of autoscanning '
                            'the runfolder. You do this by providing the final '