From: Diane Trout <diane@caltech.edu>
Date: Mon, 22 Feb 2010 20:07:21 +0000 (+0000)
Subject: there is no such thing as sequence_extended. I was using the wrong
X-Git-Tag: 0.4.0~11
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=fdea826bf42947427fd5291f2412f0e6fb4e6feb

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 f9d4e3b..0ef42a5 100644
--- 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) ]