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 e98360add54b8789ea43793de2f2cb948bd999bf..2f542bc5ac7df50f30090ad162ba2f2d3e383d3e 100755 (executable)
--- a/scripts/htsw-runfolder
+++ b/scripts/htsw-runfolder
@@ -40,14 +40,17 @@ import sys
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.runfolder import ElementTree
 
+LOGGER = logging.getLogger(__name__)
 
 def main(cmdlist=None):
     parser = make_parser()
     opts, args = parser.parse_args(cmdlist)
 
     logging.basicConfig()
-    if opts.verbose:
-        root_log = logging.getLogger()
+    root_log = logging.getLogger()
+    if opts.debug:
+        root_log.setLevel(logging.DEBUG)
+    elif opts.verbose:
         root_log.setLevel(logging.INFO)
 
     logging.info('Starting htsworkflow illumina runfolder processing tool.')
@@ -83,8 +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
 
@@ -132,6 +135,9 @@ def make_parser():
     parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
                       default=False,
                       help='turn on verbose mode')
+    parser.add_option('--debug', action='store_true',
+                      default=False,
+                      help='turn on debug logging (implies verbose)')
     parser.add_option('--dry-run', action='store_true', default=False,
                       help="Don't delete anything (in clean mode)")
 
@@ -167,10 +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 '