there is no such thing as sequence_extended. I was using the wrong

suffix generator for paired end sequencing

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index f9d4e3ba0df83a4b918a5fafcdc5e5cded75c117..0ef42a589fcdd06a90be00c4cdda4a48d10c7b02 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -140,7 +140,7 @@ def format_gerald_config(options, flowcell_info, genome_map):
             is_sequencing = True
             
         if is_sequencing:
-            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, analysis_suffix)]
+            config += ['%s:ANALYSIS sequence%s' % (lane_prefix, sequence_suffix)]
         else:
             config += ['%s:ANALYSIS eland%s' % (lane_prefix, analysis_suffix)]
             config += ['%s:ELAND_GENOME %s' % (lane_prefix, species_path) ]