mark the example submission rule files as being raw, so the escapes dont get confused

[htsworkflow.git] / scripts / htsw-runfolder

diff --git a/scripts/htsw-runfolder b/scripts/htsw-runfolder
index 7ae95b4f49ebab11f15b319647f9b19483bd1fae..2f542bc5ac7df50f30090ad162ba2f2d3e383d3e 100755 (executable)
--- a/scripts/htsw-runfolder
+++ b/scripts/htsw-runfolder
@@ -40,6 +40,7 @@ import sys
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.runfolder import ElementTree
 
+LOGGER = logging.getLogger(__name__)
 
 def main(cmdlist=None):
     parser = make_parser()
@@ -85,8 +86,8 @@ def load_run_xml_file(parser, args, opts):
     runs = []
     if opts.run_xml:
         # handle ~ shortcut
-        opt.run_xml = os.path.expanduser(opt.run_xml)
-        tree = ElementTree.parse(opt.run_xml).getroot()
+        opts.run_xml = os.path.expanduser(opts.run_xml)
+        tree = ElementTree.parse(opts.run_xml).getroot()
         runs.append(runfolder.PipelineRun(xml=tree))
     return runs
 
@@ -172,10 +173,10 @@ def make_parser():
     parser.add_option('--site', default=None,
                       help='create srf files tagged with the provided '\
                       'site name')
-    parser.add_option('--raw-format', dest="raw_format", default='qseq',
-                      choices=['qseq', 'srf'],
+    parser.add_option('--raw-format', dest="raw_format", default=None,
+                      choices=['qseq', 'srf', 'fastq', None],
                       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 '