Update save_raw_data to SampleKey api

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index eb37cc4c853af8f4d13bbadc102d4b1a8c700436..e0d84cf49fb21d3f31841ae4857e7780365db5c3 100644 (file)
--- 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 1e46e177075fb30362cb32aed6b6d9598f8010d4..67dc505f09aa878383f5ac5d3f0a6aa9de4f3f95 100644 (file)
--- 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)