Merge flowcell 'paired_end' flag from v0.1 branch

[htsworkflow.git] / htsworkflow / frontend / eland_config / views.py

diff --git a/htsworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py
index d4be4ea2e082228e32ff8b7969d585fa1e7db0b8..1d5817e86b9cdc53c9f4819e7e777756f85bdf58 100644 (file)
--- a/htsworkflow/frontend/eland_config/views.py
+++ b/htsworkflow/frontend/eland_config/views.py
@@ -307,7 +307,6 @@ def getElandConfig(flowcell, regenerate=False):
   #data.append("GENOME_DIR %s" % (BASE_DIR))
   #data.append("CONTAM_DIR %s" % (BASE_DIR))
   read_length = fcObj.read_length
-  data.append("READ_LENGTH %d" % (read_length))
   #data.append("ELAND_REPEAT")
   data.append("ELAND_MULTIPLE_INSTANCES 8")
   
@@ -347,7 +346,10 @@ def getElandConfig(flowcell, regenerate=False):
   #Loop through and create entries for each species.
   for genome in genome_list:
     lanes = ''.join(genome_dict[genome])
-    data.append('%s:ANALYSIS eland' % (lanes))
+    if fcObj.paired_end:
+        data.append('%s:ANALYSIS eland_pair' % (lanes))
+    else:
+        data.append('%s:ANALYSIS eland_extended' % (lanes))
     data.append('%s:READ_LENGTH %s' % (lanes, read_length))
     data.append('%s:ELAND_GENOME %s' % (lanes, '%%(%s)s' % (genome)))
     data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length)))