From: Diane Trout <diane@caltech.edu>
Date: Fri, 23 Mar 2012 23:53:47 +0000 (-0700)
Subject: Add fastq to the raw format add_xoption
X-Git-Tag: v0.5.5~45
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=66c4782a536c08f03e6ef4d65b6d74b351b0e995

Add fastq to the raw format add_xoption
---

diff --git a/scripts/htsw-runfolder b/scripts/htsw-runfolder
index d4310b5..e0b9937 100755
--- a/scripts/htsw-runfolder
+++ b/scripts/htsw-runfolder
@@ -174,7 +174,7 @@ 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, fastq')
     parser.add_option('-u', '--use-run', dest='use_run', default=None,