Merge flowcell 'paired_end' flag from v0.1 branch

Then use this flag in the eland_config module to specify ANALYSIS eland_pair
Also change the default analysis to eland_extended

use the following to add the new field:
alter table fctracker_flowcell add column paired_end bool not null default false;

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)))

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index 11b019e9ba01f4cbd7bc1ec446985936859ab33b..d7793fd5262b08f401f43b34ba4df259a1f338de 100644 (file)
--- a/htsworkflow/frontend/experiments/admin.py
+++ b/htsworkflow/frontend/experiments/admin.py
@@ -43,7 +43,7 @@ class FlowCellOptions(admin.ModelAdmin):
     list_filter = ('seq_mac_id','cluster_mac_id')
     fieldsets = (
         (None, {
-            'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length'),)
+            'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length', 'paired_end'),)
         }),
         ('Lanes:', {
            'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 350a74691fa76fa278e2d93dac1eaca89794d867..92b0d37b3e362b91e3932fcb426542e1784725a7 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -7,6 +7,7 @@ class FlowCell(models.Model):
   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
   run_date = models.DateTimeField()
   advanced_run = models.BooleanField(default=False)
+  paired_end = models.BooleanField(default=False)
   read_length = models.IntegerField(default=32) #Stanford is currenlty 25
   
   lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")