From: Diane Trout <diane@caltech.edu>
Date: Thu, 17 Oct 2013 21:55:14 +0000 (-0700)
Subject: Dynamically respond to the number of lanes.
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=508a497a02b31086626a7c170ce34e081ae4f640

Dynamically respond to the number of lanes.

Illumina now has single lane flowcells so the assumtion that there
will be 8 lanes is wrong.
---

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: