Use eland_extended or eland_pair instead of eland for ANALYSIS type

this required splitting up my analysis suffix for sequencing and
aligning code.

Also forcing lanes that have no available genome to be sequencing
changed part of a retrive_config test case.

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 1a5e1360d389355044c887133e699b25e088d608..136bb5a50c60ff8890a35b6b579426ca6f593257 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -116,13 +116,15 @@ def format_gerald_config(options, flowcell_info, genome_map):
     Generate a GERALD config file
     """
     # so we can add nothing or _pair if we're a paired end run
-    run_type_suffix = { False: "", True: "_pair" }
+    eland_analysis_suffix = { False: "_extended", True: "_pair" }
+    sequence_analysis_suffix = { False: "", True: "_pair" }
 
     # it's convienent to have helpful information describing the flowcell
     # in the config file... things like which lane is which library.
     config = [format_gerald_header(flowcell_info)]
 
-    analysis_suffix = run_type_suffix[flowcell_info['paired_end']]
+    analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
+    sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
     lane_groups = group_lane_parameters(flowcell_info)
     for lane_index, lane_numbers in lane_groups.items():
         # lane_index is return value of group_lane_parameters
@@ -137,11 +139,11 @@ def format_gerald_config(options, flowcell_info, genome_map):
             logging.warning(no_genome_msg % (lane_numbers, species))
             is_sequencing = True
             
-        if not is_sequencing:
+        if is_sequencing:
+            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, analysis_suffix)]
+        else:
             config += ['%s:ANALYSIS eland%s' % (lane_prefix, analysis_suffix)]
             config += ['%s:ELAND_GENOME %s' % (lane_prefix, species_path) ]
-        else:
-            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, analysis_suffix)]
         #config += ['%s:READ_LENGTH %s' % ( lane_prefix, read_length ) ]
         config += ['%s:USE_BASES Y%s' % ( lane_prefix, read_length ) ]
 

diff --git a/htsworkflow/pipelines/test/test_retrive_config.py b/htsworkflow/pipelines/test/test_retrive_config.py
index dd8f30e92d5c91f7d5b9479a2adac5592ca5d3bb..9847ffd4aea53d7a613bfe266cc882584c1c3a7d 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrive_config.py
+++ b/htsworkflow/pipelines/test/test_retrive_config.py
@@ -35,8 +35,10 @@ class RetrieveTestCases(TestCase):
         human = [ line for line in config_lines if re.search('hg18', line) ]
         self.failUnlessEqual(len(human), 1)
         self.failUnlessEqual(human[0], '345678:ELAND_GENOME /tmp/hg18')
-        unknown = [ line for line in config_lines if re.search('Unknown', line) ]
-        self.failUnlessEqual(len(unknown), 2)
+        # we changed the api to force unknown genomes to be sequencing
+        sequencing = [ line for line in config_lines if re.search('sequence_pair', line) ]
+        self.failUnlessEqual(len(sequencing), 2)
+