From: Diane Trout <diane@caltech.edu>
Date: Thu, 19 Jul 2012 18:14:29 +0000 (-0700)
Subject: Update save_raw_data to SampleKey api
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=1c62310139ce92424276ea55751318a64a8538ab

Update save_raw_data to SampleKey api
---

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index eb37cc4..e0d84cf 100644
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -439,7 +439,10 @@ class LaneSpecificRunParameters(collections.MutableMapping):
             if k.matches(lookup_key):
                 results.append(k)
         if len(results) > 1:
-            raise ValueError("More than one key matched query %s" % (str(lookup_key),))
+            errmsg = "Key %s matched multiple keys: %s"
+            raise ValueError(errmsg % (str(lookup_key),
+                                       ",".join((str(x) for x in results))))
+
         elif len(results) == 1:
             return results[0]
         else:
diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 1e46e17..67dc505 100644
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -630,7 +630,7 @@ def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1, r
 
 def save_raw_data(num_jobs, r, site, raw_format, cycle_dir):
     lanes = []
-    for lane in range(1, 9):
+    for lane in r.gerald.lanes:
         lane_parameters = r.gerald.lanes.get(lane, None)
         if lane_parameters is not None and lane_parameters.analysis != 'none':
             lanes.append(lane)