The WITH_SEQUENCE flag needs to be lower-case "true".

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 3a1a56aeaf2188350db8b980d7b098bf0098a0ba..3ba13fc715e8dd235c6ed4376eac1032be7f22f4 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -125,8 +125,7 @@ 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']
+    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)