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WITH_SEQUENCE is actually a global GERALD option, remove the lane specifier.
author
Diane Trout
<diane@caltech.edu>
Fri, 8 Oct 2010 17:32:46 +0000
(17:32 +0000)
committer
Diane Trout
<diane@caltech.edu>
Fri, 8 Oct 2010 17:32:46 +0000
(17:32 +0000)
htsworkflow/pipelines/retrieve_config.py
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diff --git
a/htsworkflow/pipelines/retrieve_config.py
b/htsworkflow/pipelines/retrieve_config.py
index c3f32c7d50e2b9dddc271e14f1b8293ec1f40e5b..d2ee8721c8f5430fde01ac0fe00425ea6fcf925a 100644
(file)
--- 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)