From 508a497a02b31086626a7c170ce34e081ae4f640 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 17 Oct 2013 14:55:14 -0700 Subject: [PATCH] Dynamically respond to the number of lanes. Illumina now has single lane flowcells so the assumtion that there will be 8 lanes is wrong. --- htsworkflow/pipelines/retrieve_config.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py index bd220a0..29f49bb 100644 --- a/htsworkflow/pipelines/retrieve_config.py +++ b/htsworkflow/pipelines/retrieve_config.py @@ -111,7 +111,7 @@ def format_gerald_header(flowcell_info): config += ['Flowcell Notes:'] config.extend(flowcell_info['notes'].split('\r\n')) config += [''] - for lane_number in LANE_LIST_JSON: + for lane_number in sorted(flowcell_info['lane_set']): lane_contents = flowcell_info['lane_set'][lane_number] for lane_info in lane_contents: config += ['Lane%s: %s | %s' % (lane_number, @@ -356,8 +356,8 @@ def save_sample_sheet(outstream, options, flowcell_info): 'Operator': format_operator_name} out = csv.DictWriter(outstream, sample_sheet_fields) out.writerow(dict(((x,x) for x in sample_sheet_fields))) - for lane_number in LANE_LIST: - lane_contents = flowcell_info['lane_set'][str(lane_number)] + for lane_number in sorted(flowcell_info['lane_set']): + lane_contents = flowcell_info['lane_set'][lane_number] pooled_lane_contents = [] for library in lane_contents: -- 2.30.2