X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fpipelines%2Fretrieve_config.py;h=3a1a56aeaf2188350db8b980d7b098bf0098a0ba;hp=fbd1187a5ca14e5517b4e8b455d3cf82c203a484;hb=86a66805c52c4bafb5d878d2b22604b9b9309cc8;hpb=b2ebef0fbd2acc0c59f006d8cad962dc47250d23

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index fbd1187..3a1a56a 100644
--- 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 +123,10 @@ 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 += ['WITH_SEQUENCE TRUE']
+    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)