From d3d535976b704bb89b993b2058a3e9bc497ee499 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 17 Feb 2009 23:45:24 +0000 Subject: [PATCH] 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; --- htsworkflow/frontend/eland_config/views.py | 6 ++++-- htsworkflow/frontend/experiments/admin.py | 2 +- htsworkflow/frontend/experiments/models.py | 1 + 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/htsworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py index d4be4ea..1d5817e 100644 --- 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 11b019e..d7793fd 100644 --- 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 350a746..92b0d37 100755 --- 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") -- 2.30.2