From: Diane Trout <diane@caltech.edu>
Date: Fri, 8 Oct 2010 17:32:46 +0000 (+0000)
Subject: WITH_SEQUENCE is actually a global GERALD option, remove the lane specifier.
X-Git-Tag: 0.4.5~1
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=d242342d007b534919ea733204853a1ad3370e37

WITH_SEQUENCE is actually a global GERALD option, remove the lane specifier.
---

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index c3f32c7..d2ee872 100644
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -125,7 +125,7 @@ def format_gerald_config(options, flowcell_info, genome_map):
 
     config += ['SEQUENCE_FORMAT --fastq']
     config += ['ELAND_SET_SIZE 20']
-    config += ['12345678:WITH_SEQUENCE TRUE']
+    config += ['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)