From: Diane Trout <diane@caltech.edu>
Date: Tue, 19 Oct 2010 19:35:57 +0000 (+0000)
Subject: Set WITH_SEQUENCE as both a per-lane AND global parameter
X-Git-Tag: 0.4.5^0
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=86a66805c52c4bafb5d878d2b22604b9b9309cc8;hp=d242342d007b534919ea733204853a1ad3370e37

Set WITH_SEQUENCE as both a per-lane AND global parameter
the per-lane version set $(lane)_WITH_SEQUENCE := TRUE in the makefiles
the gerald WITH_SEQUENCE TRUE changed the setting in the config.txt file

So lets just set both versions and hopefully we'll get sequence files
out the other end.

Let me show you my hammer...
---

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index d2ee872..3a1a56a 100644
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -126,6 +126,7 @@ 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']]
     lane_groups = group_lane_parameters(flowcell_info)