Recent IPAR xml config blocks include the runfolder name

[htsworkflow.git] / htsworkflow / pipelines / runfolder.py

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 5d1e16bce460da443da7bebea56220e388770c88..26c592ce5f7eb6d65175031f9c9010dc400d9410 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -21,6 +21,7 @@ from htsworkflow.pipelines import ElementTree, \
                                   EUROPEAN_STRPTIME, EUROPEAN_DATE_RE, \
                                   VERSION_RE, USER_RE, \
                                   LANES_PER_FLOWCELL, LANE_LIST
+from htsworkflow.pipelines.samplekey import LANE_SAMPLE_KEYS
 from htsworkflow.util.alphanum import alphanum
 from htsworkflow.util.ethelp import indent, flatten
 from htsworkflow.util.queuecommands import QueueCommands
@@ -128,10 +129,12 @@ class PipelineRun(object):
             return path_fields[-1]
 
     def _get_runfolder_name(self):
-        if self.gerald is None:
-            return None
-        else:
+        if self.gerald:
             return self.gerald.runfolder_name
+        elif hasattr(self.image_analysis, 'runfolder_name'):
+            return self.image_analysis.runfolder_name
+        else:
+            return None
     runfolder_name = property(_get_runfolder_name)
 
     def _get_run_dirname(self):
@@ -753,7 +756,7 @@ def save_raw_data(num_jobs, r, site, raw_format, run_dirname):
                 lanes.append(lane)
     else:
         # assume default list of lanes
-        lanes = LANE_LIST
+        lanes = LANE_SAMPLE_KEYS
 
     run_name = srf.pathname_to_run_name(r.pathname)
     seq_cmds = []