Some of the older flow cells used a default genome for eland instead

[htsworkflow.git] / gaworkflow / pipeline / runfolder.py

diff --git a/gaworkflow/pipeline/runfolder.py b/gaworkflow/pipeline/runfolder.py
index 1219627c2c3c5152bd8049234431f96ebc791647..19962b1d0e6e42247c57e80bdca7117736aca890 100644 (file)
--- a/gaworkflow/pipeline/runfolder.py
+++ b/gaworkflow/pipeline/runfolder.py
@@ -33,7 +33,7 @@ class PipelineRun(object):
     FLOWCELL_ID = 'FlowcellID'
 
     def __init__(self, pathname=None, firecrest=None, bustard=None, gerald=None, xml=None):
-        self.pathname = pathname
+        self.pathname = os.path.normpath(pathname)
         self._name = None
         self._flowcell_id = None
         self.firecrest = firecrest
@@ -60,7 +60,7 @@ class PipelineRun(object):
               flowcell_id = 'unknown'
               
            logging.warning(
-             "Flowcell idwas not found, guessing %s" % (
+             "Flowcell id was not found, guessing %s" % (
                 flowcell_id))
            self._flowcell_id = flowcell_id
         return self._flowcell_id