From 86a66805c52c4bafb5d878d2b22604b9b9309cc8 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 19 Oct 2010 19:35:57 +0000 Subject: [PATCH] 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... --- htsworkflow/pipelines/retrieve_config.py | 1 + 1 file changed, 1 insertion(+) 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) -- 2.30.2