Set WITH_SEQUENCE as both a per-lane AND global parameter

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...

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index d2ee8721c8f5430fde01ac0fe00425ea6fcf925a..3a1a56aeaf2188350db8b980d7b098bf0098a0ba 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -126,6 +126,7 @@ def format_gerald_config(options, flowcell_info, genome_map):
     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)