From: Diane Trout <diane@caltech.edu>
Date: Wed, 27 Oct 2010 22:51:20 +0000 (-0700)
Subject: The WITH_SEQUENCE flag needs to be lower-case "true".
X-Git-Tag: 0.5.0~20
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=84b4c04f76df1ceeabf257741c87e498c81a073f

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 3a1a56a..3ba13fc 100644
--- 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)