Set WITH_SEQUENCE as both a per-lane AND global parameter

[htsworkflow.git] / htsworkflow / pipelines / retrieve_config.py

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index c3f32c7d50e2b9dddc271e14f1b8293ec1f40e5b..3a1a56aeaf2188350db8b980d7b098bf0098a0ba 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -125,6 +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']
     analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
     sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]