Update gerald config file generation.

Include ELAND_SET_SIZE, WITH_SEQUENCE options
Stop commenting SEQUENCE_FORMAT out

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index fbd1187a5ca14e5517b4e8b455d3cf82c203a484..c3f32c7d50e2b9dddc271e14f1b8293ec1f40e5b 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -108,7 +108,6 @@ def format_gerald_header(flowcell_info):
         config += ['Lane%s: %s | %s' % (lane_number, lane_info['library_id'],
                                         lane_info['library_name'])]
 
-    config += ['SEQUENCE_FORMAT --fastq']
     config += ['']
     return "\n# ".join(config)
 
@@ -124,6 +123,9 @@ def format_gerald_config(options, flowcell_info, genome_map):
     # in the config file... things like which lane is which library.
     config = [format_gerald_header(flowcell_info)]
 
+    config += ['SEQUENCE_FORMAT --fastq']
+    config += ['ELAND_SET_SIZE 20']
+    config += ['12345678:WITH_SEQUENCE TRUE']
     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)

diff --git a/scripts/retrieve_config b/scripts/retrieve_config
old mode 100644 (file)
new mode 100755 (executable)