the per-lane version set $(lane)_WITH_SEQUENCE := TRUE in the makefiles
the gerald WITH_SEQUENCE TRUE changed the setting in the config.txt file
So lets just set both versions and hopefully we'll get sequence files
out the other end.
Let me show you my hammer...
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)